100% Achievements

This guide aims to provide the easiest methods of unlocking each achievement. Please post any questions (or comments) in the comments and I'll definitely see them.

To start off, here's a pretty full guide that covers pretty much everything else about the game:
http://steamcommunity.com/sharedfiles/filedetails/?id=782776407

Here are some useful console commands for changing the functionality of the map (changing the scale). Useful for looking for bosses and items:
Open the console with Ctrl+~

These commands are from the subreddit

I'm a Collector Myself
Unlock all achievements

You'll get these if you beat the game on the specified difficulty and they unlock as soon as you beat Ameonna.
Lower difficulties are also unlocked. For example, if you beat the game on Hard, you will also get the achievements for Easy and Normal. Casual Wang
Complete the game on Tiny Grasshopper difficulty Normal Wang
Complete the game on I Have No Fear difficulty Hard Wang
Complete the game on Who Wants Wang difficulty Insane Wang
Complete the game on No Pain No Gain difficulty These are bosses that will be defeated as you progress through the story.
King of the Dragon Mountain
Defeat Corrupted Kamiko King of Mount Akuma
Defeated Devouring Kamiko Unfinished Business
Defeat Zilla Mechanoid Goddess Slayer
Defeat Ancient Goddess Ameonna

Each of these bosses can be found during the mission stated in the description of the achievement. If you miss them, you can still find them by going to the mission selection screen and clicking Free-roam on the desired mission.
Some of these you will come across while completing missions, but most missions can be completed without ever seeing them.

I had originally given vague descriptions of where I found each boss before I realised they appeared in random places, so I can't give you exact locations. However, check the introduction section for some useful map-related console commands and keep an eye out on the map for this icon during missions: Lieutenant Akimbo
Defeat Lieutenant Akimbo in story mission: My Hero

This boss can be found during one of the two 'tutorial' missions, which means you can't come back to it. Pretty sure you have to beat him to continue though, so can't really miss him.

The Sharpest Spike
Defeat The Sharpest Spike in story mission: Hot Blooded
Vicious Sentinel
Defeat Vicious Sentinel in side mission: Chi-ters
The Chef
Defeat The Chef in side mission: The Cookery This boss must be defeated in order to complete the side mission. Frozen Widow
Defeat Frozen Widow in side mission: Ninja'd Scrolls - Part 1
The Guard
Defeat The Guard in side mission: Ninja'd Scrolls - Part 2 The Guard must be defeated to complete this side mission. Can't miss him. Unit-64 Commodore
Defeat Unit-64 Commodore in side mission: Ninja'd Scrolls - Part 3
ST-RC1 Titan
Defeat ST-RC1 Titan in story mission: Zilla Attack You'll find this boss on the way up to the top of Dragon Mountain during the story mission. Transistor ZL-260
Defeat Transistor ZL-260 in story mission: Industrial Espionage Both times I played this mission, this boss was pretty much right at the spawn. Pretty hard to miss him based on my experience. Gun Fury
Defeat Gun Fury in side mission: Demon Trafficking
Alpha R-XIII
Defeat Alpha R-XIII in side mission: Monster Tea Party
Old Fart
Defeat Old Fart in side mission: Flirty Fishing - Part 1
Shady Rascal
Defeat Shady Rascal in side mission: Flirty Fishing - Part 2
Queen of D.O.L.L.s
Defeat Queen of D.O.L.L.s in side mission: Flirty Fishing - Part 3
Apprentice of Musashi
Defeat Apprentice of Musashi in story mission: Ancestral Ties You have to defeat this guy to finish the mission. Magmator of the Devil Mountain
Defeat Magmator of the Devil Mountain in story mission: Body Shaking This story mission has a pretty small map, you'll come across this guy right away. Lord Destroyer
Defeat Lord Destroyer in story mission: All in the Family
Eradicator
Defeat Eradicator in side mission: Stop the Propaganda
The Toxitor
Defeat The Toxitor in story mission: Stop the Ooze
Captain Lo-Gan
Defeat Captain Lo-Gan in side mission: One More Thing
The Highest Priest
Defeat The Highest Priest in side mission: Heisenberg - Part 1
Colonel Fasthand
Defeat Colonel Fasthand in side mission: Heisenberg - Part 2
The Lord of War
Defeat The Lord of War in side mission: Heisenberg - Part 3
TL-Devourer
Defeat TL-Devourer in story mission: Corporate Shill
Resistor ZL-260
Defeat Resistor ZL-260 in story mission: Violent Takeover This boss is in the last mission in the game. You must fight it before you continue on to find Zilla.

Total kills across all playthroughs and all characters. Bunnies count as enemies for these achievements. Junior Hitman
Kill 100 enemies Executioner
Kill 500 enemies Call me Wang, Lo Wang
Kill 2500 enemies

I got my 2500 kills about 60% through my second playthrough, and I wasn't killing too many enemies on that playthrough.

Despite some odd wording on these achievements, you basically just need to kill enemies with damage from each element. I recommend applying the element you want to go for to your main weapon, then applying the opposing element to a similar weapon (for enemies with a resistance to your main element):
Fire and Ice are opposites.
Toxic and Electric are generally opposites somehow.
Tiny Little Pieces
Shatter 100 frozen enemies Toxic Blast
Perform 100 acid corpse explosions Living Torch
Set 200 enemies on fire Short Circuit
Electrocute 200 enemies Bullseye
Perform 100 weakspot kills

It can be tricky to know exactly what is a weakspot on enemies, though it is usually the head. Easiest way is just to go for human enemies and aim for the head.
When you attack the weakspot, it must result in a kill. Only dealing damage to a weakspot isn't enough. If you successfully hit a weakspot, you'll see a green arrow indicating the increased damage dealt.

Mr. Kosugi
Perform 50 Vanish kills

Vanish is one of your powers. When activated, you are invisible to most enemies and have high damage on your first attack. Your attack coming out of Vanish must be a kill for it to count towards this achievement. Just replay an early side mission with weak enemies and you should have no problem killing them in a single hit.

Wang the Impaler
Perform 100 kills when enemy's grasped by Grip of Darkness

Another of your powers. This one stops enemies from attacking and suspends them up on a spike for a while. You have to kill enemies while they're stuck on the spike for kills to count. The Grip of Darkness skill upgrades are useful for this as they suspend enemies for longer and add a damage multiplier.

Trickster
Perform 200 Special Attack kills

A special attack is when you move in a direction and use the secondary attack button. Sting, Vortex and Force Slash are your special attacks and each can be upgraded in the skills menu.

I Think I Saw a Wabbit
Kill 10 Bunny Lords Bunny Lords spawn when you kill a number of innocent rabbits.
The number of rabbits seem to deviate. I tested it out a little bit on Insane and it seems to happen between 3-5 rabbits killed, but it could just be random.
Rabbits appear on the map as green arrows, so it isn't hard to find them. Plus you get a bunch of loot from Bunny Lords, so it can be worth killing them past this achievement too.

You'll unlock the ability to craft at a certain part of the story, when the Smith is no longer around.

Handyman
Craft 100 upgrades

You'll find yourself with a bunch of surplus normal-quality upgrades when you're using a higher tier stuff. Crafting uses 3 of the same quality upgrades, and creates a single higher quality upgrade. Just craft all your [color=#636363]grey[/color] upgrades into [color=#1E62CE]blue[/color], [color=#1E62CE]blue[/color] into [color=#E5E51D]yellow[/color] etc.

Legendary Handyman
Craft 30 legendary upgrades

Legendary upgrades are [color=#FFA500]orange[/color]. You'll be guaranteed one of these in crafting if you use 3 [color=#E5E51D]yellow[/color] or 3 [color=#FFA500]orange[/color], but it is also possible to get a legendary upgrade when you craft 3 [color=#1E62CE]blue[/color] upgrades.

That's a Lot of Coins
Collect 1000000 zillyen

You'll likely get the 1mil achievement on your first playthrough. You find money throughout the world, on enemies and in chests.

Financial Security
Collect 10000000 zillyen

For the 10mil one, I'd recommend selling your upgrades you don't use or need after you complete the crafting achievements. Alternatively, since items bought from a store can be resold to the store for the exact same price, you can buy and immediately sell items to increase the achievement progress quickly.
For this one and the 1mil achievement, it counts all money ever picked up, no matter what you do with it once you have it.

Ready for Action
Collect 500 upgrades

You'll get this over time. You get upgrades in the world, as loot drops from enemies and from chests.

Unique Collection
Collect 200 unique upgrades

This will take you a little longer, as each collected upgrade needs to be different. There's no real point in keeping track of which you've found or anything, you'll just get it eventually as you play. I got it about halfway through my second playthrough, but it's pretty much random. Higher difficulties give you a larger range of upgrades, so it may unlock faster on higher difficulties.

Legendary Collection
Collect 100 legendary upgrades

Legendary upgrades are [color=#FFA500]orange[/color]. Higher difficulties have a higher chance of getting better loot, so playing on one of the Insane difficulties would be the fastest way to get this.

Sempai
Develop any character to level 10 Sensei
Develop any character to level 25 Grandmaster
Develop any character to level 50

Shiny!
Find 5 secrets My Precious
Find 15 secrets Ancient Chinese Secrets
Find 50 secrets Secrets in this game are found throughout missions and look like a trophy.
I'm not going to cover exact locations of the secrets as there are at least two guides covering this already. Here is a link to one of them:
http://steamcommunity.com/sharedfiles/filedetails/?id=784575949