Please give Bango some love on his post (linked above) for putting this together. I just organized it into a guide for my own quick reference while playing.

The sections of this guide are divided by where the unlockable object (chest or door) is located. The keys for that object are listed underneath them, and labeled on what floor they are located based off the in-game map.

If you find one that hasn't been discovered, or spot a mistake, please leave a comment so I can update. Thank you!

-Gate on the Wharf
Key in Mother's Stash, under floor boards (Exterior)

-Triple Circle Chest in Dining Hall/Red Salon
Key in Piaggi's Room on chimney (Second Floor)

-Five Circles Chest in Small Salon sideboard
Key in Elizabeth's Room (Second Floor)

-Earth Chest in Service Stairs
Left Key in the Garden maze on a bench next to the gazebo (First Floor)
Right Key in the Dining Hall/Red Salon in the small hallway leading to the Library (First Floor)

-Water chest in Great Conclave Chamber
Left key in Mortimer's Office (Third Floor)
Right Key in the Fire Chest (Third Floor, Mortimer's Secret Office)

-Emily's door in Chapter 2
Service key in one of the dressers (Second Floor, Emily's Room)

-Travel Kabinet in Washington's sitting room
Small key in Washington's Bedroom on chimney. (Second Floor, Washington's Room)

-Half circle chest in Elizabeth's room
Key in the food area in north west, but not initially (Second Floor, Hallway)

-Circle Chest in De Richet's sitting room
Key in your bedroom (Second Floor, De Richet's Room)

-Four Circles Chest in Jaques Peru's Room
Key in bedroom (Second Floor, Peru's Room)

-Two Coils Chest in Emily's Room
[UNDISCOVERED]

-Air Chest in Tower Room on the chimney
Left Key in the Crypt Entrance, in the round area on the floor (Underground)
Right Key in Godoy's room on piano (Second Floor, Godoy's Room)

-Four Letter Chest in Von Wollner's Room
The four letter code: ZINC

-Fire Chest in Mortimer's Secret Office
Left Key next to the box (Third Floor)
Right key [UNDISCOVERED]

-Four Letter Chest in Mortimer's Office
The four letter code: ZEUS