Choose Your Weapon Wisely (Vanilla)

Vanilla BoI comes packed with a whopping 35 activated items, of which 16 are unlocked through various achievements and such.
Amongst these 35 items, only 5-6 are best suited to the endgame, a few more are heavily suited for midgame, and the rest are almost entirely situational.

Cooldown in game is based on number of rooms required to refill the item
1 room cooldown fills 6 bars per room
2 room cooldown fills 3
3 = 2
4 and 5 restore 1-2 per room depending on the room (though it's not incredibly important since there aren't many good 4/5 room items)
6 room restores 1 per room
This means that if you have the Battery or 9-volt, longer cooldown items receive much better bonuses.

Alphabetically, these items are as follows:

3 Room cooldown
Summons 6 troll bombs randomly around the room.
Best used during: Early game
This is definitely not a favorite, nor is it incredibly useful (as it is equally dangerous to you!) it does have a few notable advantages in the early game in which is it usually easily obtainable. The primary uses for this item are to clear out rooms of enemies, heavily damage bosses and (hopefully) bust open useful rocks/secret rooms. The addition of the library in the DLC makes it even easier to find and more usable in this sense. I'd recommend using it once to save some early bombs, finish off a boss easier, etc, but don't be dragging it along from floor to floor unless you have to. 1 Room cooldown
Releases a fart cloud which poisons enemies (long poison)
Best used during: Early game
Again, not nearly top teir and with a dangerously short range, this is no favorite, but is still able to kill most anything you hit with it fairly quickly. This is usually best versus pesky knights and globins in the early/early-mid game if you aren't suited to deal with them, but again isn't worth lugging around. It charges every room so use it every room. Multi segment bosses (Larry, etc) are especially vulnerable. 3 Room cooldown
Hold the head above you, replaces next shot. Throws the head, which explodes on contact and poisons the enemy (medium poisoning)
Best used during: Early game
This one can be found in secret rooms, so it's occasionally a "flop" find, but in the early game holds the advantage of being a free bomb and heavy offense versus bosses. Otherwise, not worth the space slot. 6 Room cooldown
Using this item gives Isaac angel wings and grants flight for one room. This will instantly kill the 3rd and 4th area floor 2 bosses. Using this against the 5th area boss will instantly kill YOU instead.
Best used during: Mid/Late game
In game, this is fairly useless as there are plenty of items that do its job better, but otherwise it holds the unique advantage of being incredibly useful in obtaining some achievements.
It's hard to find (usually only appears after obtaining the Rosary) and a long recharge.
Best uses include instakilling the boss of the Depths 2 for an easy shot at a no-damage run of the depths (plus a unique achievement for finishing the boss this way!) same goes for the 4th area. Otherwise, once you've done this, there's little/no point in using it again, sadly. 3 Room cooldown
Grants Isaac a powerful damage boost, as well as boosted odds of encountering Devil Rooms
Best used during: Early-Late game
Here's an all-arounder, and definitely an item worthy of keeping all game. It's fast recharge and handy for killing bosses and pesky enemies. Pop this on a boss or on a dangerous room and watch the monsters die off rather quickly. The added effect of meeting Satan more often is even better, since it will most certainly help you become OP faster. 6 Room cooldown
Grants Isaac 1 soul heart, using it nearly guarantees your next boss will be a harbinger
Best used: Early-Late game
The book of Revelations is arguably one of the best items in the game, as it allows you to almost limitlessly generate soul hearts (essentially the games armor) on top of your normal HP. While it is a long recharge, it has little reason to be saved so consider it to be used every 6 rooms, as opposed to ready. The bonus effect of this item is a bonus chance to face Famine, Pestillence, War and Death on their respective floors as well as the Headless Horseman (and Conquest in the DLC) all of which drop relatively good items. This also makes getting one particular achievement much easier (obtaining 4 cubes of meat). The benefits to not relying on normal HP are huge in the early/mid game, as it makes using blood banks much more viable/safe, allows permanent activation of 1/2 heart items (especially the polaroid in the DLC!) and the natural accumulation of Soul Hearts is pretty useful in the late game in case tanking becomes necessary. You can never have too many soul hearts! 3 Room cooldown
Grants Isaac a shield that blocks damage for a short time.
Best used: Early-Late game
Another item well worth its weight, this book is definitely a keeper and will fight for its place in your pocket very fairly. The shield recharges pretty fast, so there's no excuse to not use it often. The advantages of the brief invulnerablility are almost limitless, but for your sake I'll list some of the big ones:
It can be a life saver
It allows for reckless attack rushes to finish off a boss
It can be used to farm a blood bank
It makes clearing gauntlets a breeze (and boss gauntlets as well in the DLC)
It makes no-damage runs so much easier! 4 Room cooldown
Spawns a random pickup, pill or tarot card
Best used: Early game
Naturally, this item is usually never worth carrying around, even in the early game, but it does give you free stuff. When you find it, use it, then leave it behind. If you happen to be on the first floor, or early in the game and have no other options, abuse it as you see fit. No reason not to! 4 Room cooldown
Copies another activated item (occasionally produces a bugged effect, but resets automatically)
0 room recharge items will also instantly recharge this.
Best used: Early-mid game
Fun, but unreliable. Definitely not a keeper unless you're out of options as it has the occasional effect of kamikaze! which will ruin your day most of the time. Has the chance of producing a 6 room effect for only a 4 room recharge, but that's about it. NOTE this can copy even items that aren't unlocked! 6 Room cooldown
Gives you a tarot card (any old card/pill will be dropped on the floor)
Best used: Mid game
This is a hit-or-miss item, as it occasionally puts out great tarots and occasionally puts out bad ones. Nearly every tarot has some use (even if its situational like the fool) so it can be handy, but the 6 room charge is a turnoff. Of course, this can also drop the Moon and the Sun cards, as well as the Stars and Death, simply put - if you know your tarot cards well than this item will serve you well with a little luck! 3 Room cooldown
"Rerolls" all treasures (not pickups) in the room into other treasures. Certain generating restrictions will be maintained (devil room items will reroll into devil room items).
Best used: Early to mid/late game
Possibly one of the best items in the game, it suffers one major flaw and that is that it is not an item to take to the end game, period. Use this until after you leave the depths, but consider dropping it before travelling any deeper!
Rerolling items is very useful at times, as it can turn trash into treasure, but it can also turn treasure into trash and ok items into trash and trash into trash and so on. Don't be a gambling addict, as it can mean passing up something useful for something useless. Play around with it for fun, but don't rely on it too heavily.

More in part 2!

3 Room cooldown
Replaces your tears with a crosshair that can be aimed by using the attack buttons. Usually very disorienting/difficult to aim.
NOTE - using the mouse for this item will cause the crosshair to move in a path from its current location towards where you are clicking (if you click/hold on your target) this is much easier to aim, but for this single-use can be a hassle.
Best used: early game
Another "meh" item, this certainly packs a punch with a very precise targetting system, but leaves you vulnerable. Can be used in place of a bomb or on bosses, but otherwise not worth the risk, especially in crowded rooms or at point blank. Cooldown N/A
Consumable! This item disappears once used and leaves your space slot empty! Once used, you will teleport to the level start and an ENTIRELY NEW floor will regenerate and reset.
Best used: Early to Mid game
Here's a gem of an item for skilled players. This item generates a new floor just for you! Now at first, this might sound bad, after all, who wants to fight another boss and more enemies? Well this also means more drops, a new treasure, new shop, new secret room, new boss/boss treasure and another shot at a devil room! That's definitely a massive benefit. Use it if you get it, but not after the Depths. Often, this is even worth the 1 heart cost of buying from Satan. 6 Room cooldown
Enemies will flee from you, you will be invulnerable, you will damage on touch and every two enemies killed while in use nets a half-heart healed back. Cannot attack during use!
Best used: Early-Mid game
This certainly packs a punch, but suffers from being less useful on bosses (less healing), and less useful on normal enemies (overall less difficult), so really overall is never quite useful anyways. At least the MLU (we'll get there later) doesn't make you chase your enemies.
Not recommended, really. 2 Room cooldown
Slows enemies and projectiles from enemies for a short time (just over 7 seconds)
Best used: Early-Mid game
Not entirely useful or useless, the hourglass will make dodging enemies and attack much easier, but overall doesn't tend to be very effective at all compared to other, more common items. 0 Room cooldown
Blows you up, dealing 1 heart damage to you, and bomb damage to enemies near you
Best used: Never
Suicide... yeah, not quite the brightest idea. It does allow you to trade hearts for bombs, but this is rarely worth it, even on floor one. You could plausibly use it to avoid taking damage/in panic situations when surrounded, but blowing yourself up usually won't solve anything, especially if the enemies in question are globins who will simply regenerate. 2 Room cooldown
Leaves a puddle at your feet, damaging enemies who cross it
Best used: when the planets allign and you're conveniently being chased by enemies who can only walk and are all coming from the same direction and plan to walk into the puddle then stand perfectly still...
Yes, one of the other bottom teir items, this one is rarely of use. Many enemies in the game hop/fly, and in a rare occasion you'll get a kill or two with this, but never as consistently as you'd think. 6 Room cooldown
Generates a random pill, drops your current pill/card on the floor
Best used: mid game
Unlike the Deck of Cards, this can give you explicitly BAD items, including stat downs. Once you've identified the bulk of the randomly generated pills in game this becomes more useful, especially if you have PhD (identifies pills and reverses bad effects into good effects) or the Luck Foot (all unidentified pills are good/neutral, no bad ones) as this means you can raise your stats fairly easily, but stops being useful if HP up isn't one of them, or if you max out those stats. Worth carrying around, but not really worth keeping. 3 Room cooldown
Petrifies all enemies for 5 seconds
Best used - early to mid game
Not entirely useful, but also not entirely useless. This item freezes enemies in their tracks for five seconds, enough time to pick off a few or to pound the living daylights out of a boss. Other than that, the overall advantage compared to other items (such as the Book of Belial) isn't that great. This can also leave you in a sticky situation when everyone unfreezes and resumes following you from odd positions, making dodging difficult if not managed properly. Overall, too short to be that good. 3 Room cooldown
Enemies will flee from you for 5 seconds
Best used - when wearing a pad on your face becomes a good idea
Another bottom teir item, this usually doesn't solve any problems you may face, as enemies fleeing to the corners of the room only means that by the time they get there they'll stop playing around and resume chasing you. Of course this means you need to chase THEM to do much anything, and when your 5 seconds are up, things are back to normal. Overall this has little benefit aside from comedic value and occasionally might leave you in a worse position that when you started! (sic)
4 room cooldown
Spawns a random familiar for the current room (including locked ones)
Best used - early to mid game
Not that useful, especially with the moderate cooldown and its situational advantages, the added firepower helps on bosses, but not as much as other items would. It's fairly rare, and most often the generated familiar will be too weak to really make much of a difference. You know what's better than a one room buddy? A permanent one. 3 Room cooldown
Drops Monstro on an enemy - Won't work if Monstro is already in the room!
Best used - early game
Mostly useless, as Monstro's aim is as bas against enemies as it is against you. If he does hit, the damage is respectable versus bosses, but he can also hurt you by accident. Pretty... meh.
Fun fact, you can kill him if you're OP/fast enough. 2 Room cooldown
Spawns Mr. Boom (a large bomb)
Best used - early game
Usually looked down upon as being rather useless, Mr. Boom can be a boon in the early game as he provides a good alternative to bombs which can otherwise be saved until later floors. Furthermore, being a large bomb means he'll also pack a heavy punch if you can land a hit on bosses. Not worth keeping though, but on the basement is worth a shot every now and then. 6 Room cooldown
Grants temporary invulnerability and damage on touch - cannot attack during use!
Best used - early to mid game
Get the laughs out of your system, we get the pun.
MLU (as it's often abbreviated) is known for being severly disliked. Now, it's not explicitly bad, but it's definitely not upper teir and is prone to replacing "good" items in secret rooms. It's got a long cooldown, but it's major benefit is of course the invulnerablility and damage on touch. Clearing rooms is a breeze with this on most occasions, and you can bum rush bosses with it too, but compared to the Book of Shadows, the length of the effect and damage done is rarely worth the extra 3 room cooldown, go figure.
Fun fact, using this with Mom's Knife WON'T prevent you from attacking, so if mutilation on touch is your style, by all means, have fun, just remember the book is still better!

More in part 3!

6 Room cooldown
Grants 1 soul heart, increases attack, decreases speed, crushes rocks you walk over
Best used - early to late game
Very similar to the book of revelations, and as such a definite to teir item worth keeping!
The nail has the added benefits of NOT summoning the Harbingers, providing an attack buff when used, and in later parts of the game (specifically area 4, where all rocks look identical and are often in great quantities) the rock crushing bonus can actually yield some fun prizes out of magic rocks. Otherwise, it's slightlly more situational and sometimes rarer, but depending on your preference is a match for or better than the already useful book of revelations! 6 Room cooldown
Deals heavy damage to all enemies on screen
Best used - mid to late game
This item pretty much wipes out the room, enough said right there. Against bosses, it's hardly as useful, but multi segmented bosses will feel the pain even more. If you augment this with the Battery or 9-volt it becomes a viable end game keeper, but still not as useful as some others might be. Of course, towards the end game, there will always be that nightmare room you just don't want to fight through (or if you abuse the gauntlet spawning bug) this book let's you do just that - kill everything right away.
NOTE - globins won't be instakilled by this, nor will hosts unless they are raised. Globins will, however be reduced to piles of goo, but will regenerate very quickly (almost immediately). 4 Room cooldown
Charges across the room, granting very brief invulnerability and damage on touch
PASSIVE - grants flight and increased speed
Best used - early to mid/late game
Let's face it, this is what you all really want.
This is sometimes a keeper, but only if you don't otherwise gain natural flight through another item (such as transcendence). The extra speed is also incredibly nice. The charge isn't an A+ effect, and usually does little or nothing but pick off one or two enemies, but it's really not the focus of this item. The focus here is the flying and speed, and in those categories this item delivers. This makes dodging and self defense much easier, flight being one of the more desirable in game effects, but it costs you the space slot.
I'd recommend it in the late game ONLY if you have no other flying items. (They're much more common in the DLC, so this item becomes even less useful)
Fun Fact - sometimes this item is worth it for the visual effect alone... 1 Room cooldown
Drops a pile of poop at your feet
Best used - as a last resort
This item is ironically **** teir. You can slow enemies down by making them walk around it, sometimes they'll get caught and stumble around it awkwardly, and in a one in a million situation you can block an enemies path entirely. This also can serve as a shield from enemies who shoot at you, but this is also incredibly situational. The poop rarely also gives a random pickup from the poop destroyed. That's all there is to be said. Just trade it for something else when you can. 0 Room cooldown
Shaves off some HP (ouch!) in exchange for a damage boost, which is stackable. Costs more HP to use the deeper you go!
Best used - ...
How often will the HP lost this way be worth the temporary damage boost? If you have tons of soul hearts and a reliable supply of normal hearts to refill the lost HP, you might make some use of it, but otherwise it's not really that good. Mind you this item CAN kill you if you shave off too much. 6 Room cooldown
Cuts off your head... grants flying (as a floating head) and a fast moving, auto attacking familiar (the body)
Best used - early to mid game
The flight is usually just an excuse to go fly over a hole and hide somewhere safe as the body familiar here moves very fast and hits really hard. Against bosses this is usually quite useful, but the 6 room charge can make it pretty situational otherwise. As you enter the late game, this is still only moderately useful. 3 Room cooldown
Fire ur lazur
Best used - early game
This leaves you vulnerable before and after firing, and has a delay before the beam actually fires, but still packs a reasonable punch for a 3 room recharge item. If you can get the hang of it, it is occasionally worth the laugh, but otherwise you're typically better off ignoring this one as the beam will rarely solve the problem of being swarmed with enemies. So it's not good against a lot of little enemies and it's mediocre against big ones, that's about it. 1 Room cooldown
Fires a ring of 10 projectiles around you
Best used - early to mid and sometimes late game
Often overlooked as an item, this is usually a lot better than people give it credit for. It's difficult to aim (usually it's more luck oriented) but the attacks do quite a lot of damage against normal eneimes (not that much against bosses) but one room recharge means you can crank this thing out in every room, which means on average that you have one or two less enemies to deal with in every room. Early on, this can be great! Of course, this item also maintains some abilities you have with your tears, so some effects like My Reflection, Ouija, Spoon Bender, etc. which modify tears can often have a massive benefit to Tammy's Head. Otherwise, it's entirely preference whether you feel this is worth dragging along to the late game.

Part 4 is it for Vanilla items!

2 Room cooldown
Randomly teleports you to another room.
Best used in - early to mid game
This is a very unpredictable item. It can drop you into the secret room, into a locked gauntlet room, into the shop or treasure room, into a room full of enemies, or even into the boss room, so consider it both useful and dangerous. Of course, this can pull you OUT of danger and put you INTO more danger, but it cools off fast, so use it often if you can handle the risks. Don't use this on the Depths 2, but feel free to fight the boss there THEN use it to get out. The best uses for the Teleporter in general tend to be as either an emergency escape option, or as a way to steal items from gauntlets without having to fight through the subsequent waves of enemies. 6 Room cooldown
Opens a trapdoor to the next floor
Best used in - see situations below
Naturally you should never use this item, as it's almost never worth it except for the following rare situations:

1. You want a no-damage run and are skipping floor one of the area (don't skip floor 2, you won't get the achievement).
2. You know you cannot beat the boss on this floor, but can definitely handle the next floor.
3. You want to beat area 4 before finishing area 3 for the first time (hardcore!)
4. You want to guarantee a door to area 5 before unlocking it (also for the brave!)
   Otherwise it's more of a handicap to pass up on treasures.

4 Room cooldown
Heals one full heart
Best used in - early to mid game
Once you get soul hearts, this is immediately less useful. In fact, one soul heart (guaranteed to be useful) is always better than one normal heart except for using on blood banks. Consider the Book of Revelations and the Nail to be a direct upgrade to this, but don't forget that in the early game, this can still be occasionally useful, just not THAT useful. Not really a keeper unless you're death prone, and even then this still won't be your lifesaver - see the book of shadows for that department.

Come back soon for the WotL section!

My top picks for end game items (in somewhat of an order of use):
Book of Shadows
Book of Revelations
The Nail
Book of Belial
A Pony (vanilla only)
The Necronomicon
Tammy's Head