I had a lot of fun with this game, especially finding its various secrets. Although I haven't gotten them all yet, I figured since there wasn't an achievement guide yet, I'd put one together. With new games like this with so many secrets, it can be tough to find leads early on, so hopefully this can help someone out.

I'd highly encourage you to take a crack at the secrets yourself before using the guide. I'll try to include some hints if you need help along but still want to try solving it yourself. These were really cool to stumble across and clearly had a lot of effort put in, so it's worth trying for yourself!

Feel free to comment to correct me on anything, and I'll edit the guide with any corrections.

Also, spoilers ahead. I'll spoiler tag any major ones but certain character names and locations will be revealed.

These are all achievements that should be unmissable through regular progression through the game.

Blasphemer
Awarded on desecrating the first altar.

Upstepper
Awarded on leaving the crypt.

Royal Flush
Awarded on getting past the rat guarding the palace using the crowns.

Iconoclast
Awarded upon helping Ulara get the books of the four lost gods.

It Burns!
Awarded upon stepping into the sunlight at the temple.

These are achievements you get by beating various characters in Whatever.

Beginner's Luck
Awarded upon beating the Cryptmaster at Whatever.

Even Steven
Awarded upon beating Steven at Whatever.

Out for the Countess
Awarded upon beating Countess Ulara at Whatever.

Card Magic
Awarded upon beating Orthos at Whatever.

For these ones, you'll need to find all of the characters' hidden skills. However, it's likely by the end of the game you won't have all of them unlocked; I only had half unlocked by that point. So if you want these, you'll probably have to grind a bit for them.

Man of War
Restore all of Joro's memories.

Lady Killer
Restore all of Syn's memories.

Melody Maker
Restore all of Maz's memories.

Sorceress Supreme
Restore all of Nix's memories.

These are achievements that are missable through the playthrough, but are straightforward to get if you follow their quests. Also, achievements that you get at specific points where you get to make a choice.

Here Come the Brides
Awarded upon marrying Goggo. When given the option between Lovejuice and Sleepjuice, choose Lovejuice. I believe you only get this one if you use Lovejuice. If someone who used Sleepjuice can confirm/correct this, I will edit this.

Goodnight, Sweet Prince
Awared upon putting Goggo to sleep. When given the option between Lovejuice and Sleepjuice, use Sleepjuice. Note: I believe these two are currently mutually exclusive. I used Lovejuice, and have not seen any opportunity to go back and use Sleepjuice, unless maybe you're able to quit before the choice is saved. Will edit if this changes or I'm corrected.

Stinkbomb
Awarded upon digging up Ratty's treasure. In the quest given by Ratty's father, find Ratty and use the "Dig" command where his treasure is hidden. If you're having trouble finding it: It can be found in a corner in the room with the entrance to the Pools.

Brew Master
Get the Portable Cauldron. Awarded upon bringing Ratty back to his father.

Special Delivery
Deliver the Piper's diss track to Ulara. Awarded upon playing the wax cylinder in her chamber.

Grateful Undead
In the ending, when given the choice between "Kill" and "Smash", choose "Kill."

Paragon
In the ending, when given the choice between "Kill" and "Smash", choose "Smash."

These are achievements that are either straightforward but pretty easy to miss in a regular playthrough, or fairly complicated secrets.

Bragging Rights
Catch a rare fish. There are five of these that I know of in various locations in the game. These fish will generally have pretty different names than the ones you typically catch, so they're hard to miss.

Locations Found: Bridge, Sea Caves, Rumpus, Underwood
Names of Fish Found:
Agathadaimon
Decolletage
Echolalia
Lazaretto
Zugzwang

Pottymouth
Unlock the swear jar.
Hint: The solution to this should be pretty intuitive, just think of why you'd need a swear jar.
Solution: Just curse a bunch. I'm not sure the exact amount of times needed, but eventually the Cryptmaster has had enough and will give you a swear jar. Every time you curse from then on, one soul will go into the swear jar.

Repeat Offender
Get sent to the cage two times at the Gate. You can get sent into the cage either by going up to the gate itself before every member of the party has gotten paladin helmets, or if you go to the gate with the paladin helmets and Give anything other than a number 1-6 for which squad you're a part of.

JSN
These spoilers relate to the ending of the game.

Hint #1: There are more than two choices you can make during the ending.

Hint #2: If you play Orthos in Whatever, he'll give you a hint that might be helpful.

Hint #3: Orthos speaks of a short, powerful, and ironically, positive word. What short word might be a better choice than the two you're given in the ending?

Hint #4: "JSN" itself is an acronym. What could it stand for? The word you need is in here.

Solution: When presented with the option to "Kill" or "Smash" in the ending, instead, simply say "No."

Clickety Click
This secret is twofold. It's a bit tucked away, but still relatively easy to find the first part if you've been exploring. You can get this after you've visited Pantry.

Step 1: Find the hidden location.

Hint #1: Search the Sea Caves

Hint #2: The northmost entrance in the Sea Caves hides a well.

Hint #3: The well's sign is written in Payn's language. Try translating it once you've gotten the language deciphered for Ulara's quest.

Solution: The name of the hidden location is "Mornay". Type this and it should open a portal.

Step 2: Appease the Crab King.

Once you've found the word for the hidden location, you'll be transported to an island inhabited entirely by crabs and crabmen. You'll want to simply follow the path to the end of the island, where you'll find a cave with the giant Crab King inside. Approach him, and he'll try to speak to you. Only, he speaks entirely in Clicks and Clacks. You'll need to figure out what to say to him.

Hint #1: There's a pattern to the clicks and snaps that can be translated. What the Crab King is saying is the word you'll need to repeat back.

Hint #2: Try to think of a notable language/pattern where there's only two possible characters. Think about substituting "Click" and "Snap" for more familiar characters.

Hint #3: The Crab King is speaking in binary, the "Clicks" correspond to 0 and the "Snaps" correspond to 1. Enter this into a binary translator to get your answer.

Solution: The Crab King is saying "Hey". Say "Hey" back to appease him, and get the achievement. As an added bonus, you get his Whatever card. In addition, if you say "Hey" to a Crab man during combat, they will become peaceful. If you say "Hey" to the regular crabs, they'll click you out a little song.

Legendary Angler
To get this, you must find the Master Rod. If you're looking for a place to start with this, try the "Bragging Rights" achievement.

Hint #1: You cannot find the Master Rod in any of the regular game locations. You must find a secret portal word.

Hint #2: Each of the 5 rare fishes carries a ring with a corresponding letter. These letters will help you find the word.

Hint #3: In alphabetical order, the rings/letters you can find are:

A
D
E
L
Z

Solution: The secret word you're looking for is "Zelda". Type this in and you'll get a portal to the location with the Master Rod, and get the achievement. I'm not quite sure if the master rod has any mechanical differences.

Snooper
Thanks to Galo348 in the comments for the hint on this one!

This is awarded when you find Countess Ulara's secret room.

Hint #1: If you ask Countess Ulara herself for the secret, she'll give you a hint.
Hint #2: You'll need to "Push" the bookcase in question.
Hint #3: If you try to read the bookcase in question, the Cryptmaster won't let you.
Solution: "Push" the Erotica bookcase in the library. This will open the barred door in the library, where you can get the achievement.

Refuser
Thanks to the devs and folks in the comments for the advice on this one!

To achieve this, have the Cryptmaster walk you through how to get a refund.

NOTE: To get this, you'll need to be at the start of the game. If you're already in a save, make sure it's backed up before you get this so you can restore it afterwards.

Your save files can be found in Users\[UserName]\AppData\LocalLow\PaulHartandLeeWilliams\CryptMaster. Just make a copy of these and replace them after you're done with this.

Hint #1: Make the Cryptmaster think you don't know what you're doing.
Hint #2: You'll need to progress up to the first enemy.
Hint #3: Ignore all warnings and tooltips.
Solution: Progress to the first enemy without unlocking Joro's "HIT" Skill; the Cryptmaster will scold you, and you'll unlock the achievement.