The following is a list of items and actions that can be done in the various rooms.

1F
Cathedral
Pipe Organ: use gear, sun paper, moon paper, flower paper, girl paper, mother paper.
The Altar: key of trials
Bottom right cluster
Room of Trials: touch smiling child (insert six gems from Room of Destruction, Purification, Sorrow, Benediction, Condemnation, Life)
Past Sun Door
Stairs to 2F
Room of Carvings
Room of Pictures
Warehouse: elixirs, 2x4s
Room of rubble: Hammer
Room of rubble
Armory: Proximity mines
Past Moon Door
Central Management Room: Password is 0319
Courtyard Water Fountain: Bullets, grate to downstairs
Courtyard Storage: Use gun on door (flashlight, blanket)
Courtyard Greenhouse (large): Use crowbar on door
Courtyard Greenhouse (small): pistol
Pethouse: Grate key, girl paper
Water fountain room: Garden key (use crossbow at the top of the fountain after using the neutralizer)
Stained glass: Use crowbar
Garden: Touch red flowers, obtain flower paper and mysterious key (R)
Ruins
Laboratory 1: Read
Laboratory 2: Read
Generator room: Go upstairs

2F
Private room 1: Touch vase
Private room 2: Moon paper
Private room 3: Military gloves

B1F
Laboratory A (storage)
Laboratory A-2: Make neutralizer
Laboratory A-1: Use rock, obtain boots
Laboratory B-1: Open B-2 door
Laboratory B-3
Laboratory B-2
Laboratory B-4: Use serum, obtain gas mask
Laboratory C-1: Hook, winch
Laboratory C-2: Cord
Laboratory D-4: Hints about Lab D
Laboratory D-1
Laboratory D-2: Put out fire
Laboratory D-3: Obtain sun paper from safe (at bottom of screen)
Devil Statue: Golden key
Elevator (W): use cord
Resting Room: Security Office Key
Security Office: Move shelf to reveal poster
Storage room: Bolts, bullets, grenades
Specimen room 1: Rope
Specimen room 2: Flare
Specimen room 3: Bundle of keys
Specimen room 4: Lab coat (with drawer key)
Pantry: Shovel, towel
Kitchen: Use flare, hose
Hall: Blue spear key
Pool control room: Obtain pool key
Culture pool: Use gas mask before entering, obtain main conference room key
Main conference room: Use flashlight, obtain mysterious key (L)
Storage room door: Use crowbar and crossbow
Storage room (blue, green, red): Use respective colored spear keys
Large office: Green spear key
Door to residential area: 0512
Toxic Hallway
Equipment room: Iron ball
Locker room
Men's bathhouse: Crowbar
Women's bathhouse: Chains
Developing room: Curtains
Training room
Shooting range: Use curtain, obtain crossbow
Front desk: Blankets
Elevator (E): Use cord
Maintenance room: Find Frasier's birthday (March 19)
Stained-glass room: Use gun, obtain red spear key

B2F
Room woke up in: Use dog key
Pinned corpse
Key hanger: Dog key
Dog door: Use dog key
Archives: Pull the "correct" book
Operation room: Crank
Body disposal room: Use stone with luminating liquid on hole
Exam room
Switchboard: Turn on the normal button
Cell: Old hammer
Sacha's corpse: Key card
Confined cell: Exam room key
S Shutter: Look here for hint
Sculpture (people dancing)
Sculpture (asking for forgiveness): Use old hammer
Sculpture (people working)
Electrical control room: Use keys for lifts and shutters
Slashing torture room: Knife
Water torture room: Fuel tank, block of ice
Fire torture room: Melt block of ice, obtain W elevator key, matches
Hanging torture room: Mirror of prayers, cloth
Drug torture room: Ethanol, matches
Electrical torture room: Pliers, matches, e elevator key
Corpse near the northwest door: Hint for opening northwest door
Northwest door: From bottom, donkey, dog, cat, chicken.
Walk-in freezer: Frozen towel
Storage room: Hose
Kitchen: Fuel tank
Dining room: Blowtorch
Pantry (lower floor)
Pantry (middle floor): Chicken key
Pantry (upper floor)
Chicken door: Use chicken key
Power plant controlling device: Plastic explosives