Items

Antlers

Found: Just past the defeated Warden
Uses: Punctures one of the Behemoth's veins.

Bag of Seeds

Found: Courtyard, on the table in the Shack.
Uses: plant in the patch of soil in the Fallow Grounds (Past).

Black Eye

Found: Locked cell in the Cell Block
Uses: solves the fourth Djinn riddle.

Bronze Cup

Found: Courtyard, in the Ruined Tower
Uses: Fill with some acidic sap to dissolve the padlock on the Bridge Clearing cell.

Chains

Found: Cell Block, in a jail cell on the other side of the passthrough cell.
Uses: Moves large lever in the Sewer, holds movable armor in place, fixes wheel crank mechanism in Lava Chamber.

Cloak

Found: Turret (Present)
Uses: Protection against Fire and Ice spells when equipped.

Crystal

Found: Isolated Room
Uses: mount on the pedestal in the Crystal Hall

Crystal Shard

Found: Entrance (Caves), on the ground
Uses: Help to redirect light shining into the Grotto

Glass Cover

Found: One of the rooms in the Mirror Chamber (labeled as Unscorched Prism on the map), on the ground by some crates and barrels.
Uses: protects the Prism from being harmed by fire.

Golden Key

Found: Throne Room, near the throne
Uses: Unlocks the door in the Library Hallway

Hammer

Found: near the gear mechanism in the Dining Room
Uses: smash the crumbling wall in the Study

Hammer Handle

Found: use the Hammer
Uses: attach to the slot in the Turret (Past) to create a lever.

Helmet

Found: Lower Tunnels A (Caves), on the ground
Uses: Complete a set of armor in the Armor Room of the Caves.

Imp's Skull

Found: Turret (Present)
Uses: Solve the first Djinn riddle.

Key

Found: Fire Pillars room (Elemental Tower) on the floor; Cell Block (Dungeon) in a cell near the railing
Uses: unlocks the door to the Scriptorium; unlocks the door in the Dungeon Dining Room

Lantern

Found: Courtyard, one is on the bottom of the balcony stairs and the second is in the Shack closet.
Uses: half the items needed to unlock the Study

Left Medal

Found: Armory, on the stone bench
Uses: half the items needed to unlock the Study

Metal Bar

Found: Small area between Library and Library Annexe, after stopping the waterfall
Uses: Pries open the door in the Crystal Room, acts as a lantern hold in the Caves.

Moon Pendant

Found: Armor Room (Caves), on the ground just past the melted ice wall
Uses: gives access to two doors in the Caves

Old Rope

Found: On some barrels on the Wall Walk
Uses: string across the gears in the Dining Room in the Elemental Tower

Old Tome

Found: On a bookshelf in the Library
Uses: Solves the second Djinn riddle.

Prism

Found: Various time period within the Mirror Chamber
Uses: Protect this from harm to open a new exit to the chamber.

Right Medal

Found: Dining Hall, on the fireplace mantel
Uses: half the items needed to unlock the Study

Scroll

Found: On a bookshelf in the Library
Uses: Disables the protective blue barrier guarding the Archivist.

Set of Bolts

Found: Study in Elemental Tower, Parapet Bridge
Uses: Create footholds in the Turret Stairs, load the crossbow.

Skull Flower

Found: Courtyard, grown in the soil of the Fallowed Grounds (Past)
Uses: Solves the third Djinn riddle.

Small Twisted Key

Found: Given by Djinn along with the fourth riddle.
Uses: Unlocks the only locked cell in the Cell Block

Stone Disk

Found: Quarters B (Dungeon), on the floor near a smashed bookcase.
Uses: unlocks the door with the iron ring in the Cell Block

String

Found: Crystal Room, on the floor. About halfway between the door and the crystal pedestal. Make sure you're looking at the floor, otherwise this might not highlight.
Uses: strings the crossbow

Time Orb (Deactivated)

Found: You start with this
Uses: No use

Time Orb (Activated)

Found: Defeat the Djinn
Uses: Activates pink time crystals to allow limited local time travel.

Wooden Key

Found: Lab, being held by the hanging skeleton
Uses: unlocks the device in the center of the Library

Yorick

Found: In the right slot outside the Study door, in the Middle Hallway
Uses: gives you semi-useful hints sometimes