Unless I am missing something, this guide is now complete.

This guide was made for Light Puzzle Difficulty, and some codes change based on the difficulty. By quickly listing it here it should help speed up playthroughs if you want to go for achievements (like completing the game under 10 hours) or quickly earn a specific ending.

For Light Puzzle difficulty, these codes do not change.

Grand Market Keypad code: (Optional) Gives health and handgun ammo
4442

Hidden Glyph room:
15-11-13

3-Coin Puzzle Solution:
Man Maiden Flower
Sword Maiden Serpent
Serpent Grave Man
The true sinner is the Man*
(For the sinner portion, any coin works to solve the puzzle, the only change is which ending will gain a point.)

Clock puzzle: (In case the hint changes)
Henry is 9
Mildred is 2
Scott is 3

Butterfly puzzle:
582
or
5 circles, 8 moons, and 2 skulls

First Key lock:
287

Nurses' Station:
3578

Mannequin Arm:
92-45-71

X-ray code combination
4-37-12

Book Shelf code:

Fancy puzzle in Director's Office:

Otherworld:

2/3 codes for super lock-box:
Combination
1622

Pin number box
9659

Contest Decorative box puzzle (Optional)
231

Historical Society trap room:
932

Weight puzzle:
Equilibrium:

Hanging puzzle:
2

Note: For the following area, Labyrinth, there is only the rotating room puzzle. Just match the door number to the corresponding symbol on the lit-up wall. It will be correct if you can see a bridge connect from the square to the next area.

Bookshelf book symbols: (from left to right)
Wings Bull Lion Hawk

Briefcase
DARK WISH

Basement Keypad Code
7414

Lobby Figurine riddle puzzle: (turn each key that many times)
7-2-1

Thanks for reading! I wanted to create a quick list so simple codes or combinations can be solved faster, since there are moments where you follow multiple steps for a code. I hope this was helpful, and if I missed anything, (or got a code wrong because I typed the wrong digit) then let me know so I can fix it!