When navigating between rooms, I'll give a direction if you're just going from one room to the next. If you need to traverse more than one room at a time, I'll just give a destination.

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Ok, here we go.
ROOM 3 (Start)
Crystals:
Left side, in trees.

Zoom in on car.
Crystals:
On seatbelt holder.
Actions:
Read newspaper.
Get OLD KEY under steering wheel.
Zoom out, and go north to ROOM 7.

ROOM 7
Crystals:
Left side of railing.
Go east to ROOM 8.

ROOM 8
Crystals:
On left, in broken door.
Actions:
Optional: Zoom in on purse, read ID card, and zoom out.
Pull rope hanging right of gate.
Go west to ROOM 7.

ROOM 7
Actions:
Examine hole in right side of bricks; get MAP.
Use KEY on door.
Go north to ROOM 12 (main lobby).

ROOM 12
Crystals:
On floor to left of stairs.
On floor to right of stairs.
Top of left column.
Top of right column.
Go west to ROOM 11.

ROOM 11
Crystals:
Top-left, on wall.
Ceiling, above window.
Go south to ROOM 6.

ROOM 6
Crystals:
Middle-left, on door.
Top-right, between windows.
Middle, on window.
Actions:
Get COG 1 from bottom of wheelchair.
Go south to ROOM 2.

ROOM 2
Crystals:
Top-left, on wall.
Top-right, below window.
Actions:
Get AXE from table.
Go west to ROOM 1.

ROOM 1
Crystals:
Lower-right, on floor.
Actions:
Get FUSE from floor (top, near drain).
Go north to ROOM 5.

ROOM 5
Crystals:
Left side, on floor.
Middle, on chair.
Right side, near back wall.
Go back to ROOM 11, then west to ROOM 10.

ROOM 10
Crystals:
On window (left side).
On window (upper-right side).
On window
Go west to ROOM 9.

ROOM 9
Crystals:
Left side, under bed.
Right side, behind desk.
Top of window.
Actions:
Get SCREWDRIVER from desk.
Zoom in on clock, and make screenshot for later.
Go south to ROOM 4.

ROOM 4
Crystals:
On wall to the right of leftmost door.
On rear wheel of wheelchair.
Actions:
Click leaves, then click diagram under them, and make screenshot for later.
Go back to ROOM 12 (main lobby), then go east to ROOM 13.

ROOM 13
Crystals:
Left wall, above graffiti.
Right wall, above graffiti.
Go north to ROOM 20.

ROOM 20
Crystals:
On left bathtub.
Go south to ROOM 13, then east to ROOM 14.

ROOM 14.
Crystals:
Right side, in green drawer.
Actions:
Take JOURNAL from cabinet; read through it for important clues.
Open top-left drawer of file cabinet. Read files for two codes:
Full access: 4578
Partial access: #3435
Go east to ROOM 15.

ROOM 15
Crystals:
Bottom, on white square.
Top, in 1st row, 4th column.
Actions:
Use FUSE in empty slot, then tighten with SCREWDRIVER. This turns the power on.
Go west to ROOM 14.

ROOM 14
Actions:
Click the door, and enter the code 4578.
Go north to ROOM 21.

ROOM 21
Crystals:
On mirror.
On desk.
Bottom, under desk.
Actions:
Get JOURNAL PAGE from desk. Read new page (optional).
Ignore the bottle, can't do anything with it yet.
Go back to ROOM 12 (main lobby).

ROOM 12
Actions:
Click the door, and enter the code #3435 (remember the "#").
Go north to ROOM 19.

ROOM 19
Crystals:
Ceiling, above arch.
Ceiling, further down the hall.
Go north to ROOM 24 (church).

ROOM 24
Crystals:
Left side, below window.
Right side, on window.
Go east to ROOM 25.

ROOM 25
Crystals:
Top, to left of door.
Top-right, above right door.
Bottom-right, left of right door.
Go north to ROOM 31.

ROOM 31
Crystals:
Left side, on wall.
On right wall, in bright spot.
Go south to ROOM 25, then east to ROOM 26.

ROOM 26
Crystals:
Left side, on blue wall.
Right side, above sinks.
Bottom, on fallen lamp.
Go east to ROOM 27.

ROOM 27
Crystals:
Top-left corner of bed springs.
Wall above door.
Under checkerboard (get it first).
Actions:
Get CHECKERBOARD from floor.
Go north to ROOM 33.

ROOM 33
Crystals:
On bathtub faucet.
Top of window.
Sink faucet.
Actions:
Get JOURNAL PAGE from floor; read it (optional).
Go south to ROOM 27, then east to ROOM 28.

ROOM 28
Crystals:
Top-left, on wall.
Middle, green wall under pictures.
Go north to ROOM 34.

ROOM 34
Crystals:
Bottom-left, under bed.
Middle, on wall.
Ceiling, on light.
Actions:
Zoom in on Christmas carols under bed; make screenshot of "12 Days" song.
Go back to ROOM 26, then go north to ROOM 32.

ROOM 32
Crystals:
Bottom-left, on wall.
Bottom-right, on wall.
Go north to ROOM 36.

ROOM 36
Crystals:
Top-right, on wall.
Bottom-right, in rectangular structure.
Actions:
Get COG 2 from right rectangular structure.
Go east to ROOM 37.

ROOM 37
Crystals:
Above door.
Right side, on wall.
Middle-top, just to right of door.
Actions:
Drag lower-right debris away, and get COG 3.
Go west to ROOM 36, then north to ROOM 38.

ROOM 38
Crystals:
Right side, on window.
Go east to ROOM 39.

ROOM 39
Crystals:
Right side, on wall (left of vines).
Actions:
Tear off both sections of wallpaper.
Use AXE on bricks to reveal wall with empty slots.
Put three COGS in slots, to reveal secret door.
Go north to SECRET ROOM.

SECRET ROOM
Crystals:
Top of stand to left of chair.
Middle of stand behind chair.
Top of stand behind chair.
Right window.
Actions:
Get MIRROR from chair.
Zoom in on portrait. Flip portrait over and get STAINED GLASS 1.
Go south to ROOM 39, then east to ROOM 40.

ROOM 40
Crystals:
In trees outside right window.
Actions:
Get SHOVEL on right.
Go all the way back to ROOM 19, then go west to ROOM 18.

ROOM 18
Crystals:
On open door in background.
Above same door.
Ceiling.
Go west to ROOM 17.

ROOM 17
Crystals:
Top of window.
Left of window.
Sink faucet.
Go west to ROOM 16.

ROOM 16
Crystals:
Top-left, on left door.
Actions:
Zoom in on "true love" paper in stall; make screenshot for later.
Move dark tile on stall wall, and get STAR KEY.
Go back to ROOM 18, then go north to ROOM 23.

ROOM 23
Crystals:
Top-left, above window.
Middle, at end of hall.
Bottom-right, on floor.
Go west to ROOM 22.

ROOM 22
Crystals:
None yet
Actions:
Get WOODEN PEG 1 from desk.
Go north to ROOM 29.

ROOM 29
Crystals:
Top-left, on wall.
On window.
Bottom-right, on floor.
Bottom-middle, on white square.
Actions:
Click two knobs on left wall, to open trapdoor.
Climb down ladder to TUNNEL 1.

TUNNEL 1
Crystals:
Left side, wall left of stairs.
Go east to TUNNEL 2.

TUNNEL 2
Crystals:
Bottom-right, under table.
Top-right, on wall.
Actions:
Get ROPE from table.
Go north to TUNNEL 3.

TUNNEL 3
Crystals:
Left wall.
Top-left, on ceiling pipes.
Actions:
Get JOURNAL PAGE on left; read it (optional).
Go north to GRAVEYARD.

GRAVEYARD
Crystals:
Bottom, next to closest grave.
Right, above third grave.
Actions:
Use SHOVEL to dig in front of middle row, 4th grave; get STAINED GLASS 2.
Go back through tunnel to ROOM 29. Then go back to ROOM 23, and north to ROOM 30.

ROOM 30
Crystals:
Left side, on floor.
Right side, wall above stairs.
Actions:
Get RUBBER DUCK from bathtub.
Zoom in on paper on board.
Order items correctly (tilde will turn brown when item is correct).
When all are in correct order, make screenshot for later.
Go north to ROOM 35.

ROOM 35
Crystals:
Lower-left, on floor.
Top, on wall left of window.
Actions:
Zoom in on orange picture. Click SCREWDRIVER on orange stems, to reveal puzzle.
To solve puzzle:
Look in JOURNAL for patient who packed orange crates.
She kept reciting a list of numbers. Notice that these numbers are in 4 pairs, and each pair skips a number. That skipped number must go into the code. For example: First number pair is "27, 29", so the code number is 28.
Final code: 28, 44, 15, 86.
After entering code, push black button to get STAINED GLASS 3.
Now we start backtracking and solving puzzles. Go to ROOM 31.

ROOM 31
Actions:
Solve the infamous ball puzzle, using screenshots of "12 days" Christmas carol and "true love" paper from bathroom.
Solution is:
8: top left
7: top right
1: middle right
2: bottom left
5: bottom right
Then use STAR KEY in keyhole, and click key again. Get STAINED GLASS 4.
<Solution originally found by Jess from Freegamesnews.com>
Go to ROOM 32.

ROOM 32
Actions:
Solve the symbol puzzle, using the screenshots of the clock and meal schedule you took earlier. Get OLD KEY.
Go to ROOM 38.

ROOM 38
Actions:
Zoom in on right hole, and use ROPE on object in hole to get HAMMER.
Go to ROOM 17.

ROOM 17
Actions:
Use HAMMER on broken window. Get WOODEN PEG 2 from floor.
Go to ROOM 20.

ROOM 20
Actions:
Put RUBBER DUCK in pool. Get STAINED GLASS 5.
Go to ROOM 14.

ROOM 14
Actions:
Use OLD KEY on file cabinet, 2nd row, 1st drawer. Open drawer and read files. One contains a RAZOR.
Go north to ROOM 21.

ROOM 21
Actions:
Zoom in on medicine bottle, and use RAZOR to remove label. Then click bottle cap to get WOODEN PEG 3.
Go to ROOM 8.

ROOM 8
Actions:
Put CHECKERBOARD in slot. Ghost gives you STAINED GLASS 6.
Go to ROOM 22.

ROOM 22
Crystals:
Inside cupboard (after opening it).
Actions:
Put 3 PEGS into holes, then pound each one in with HAMMER. Cupboard opens to reveal puzzle.
Solve puzzle by making pattern match screenshot taken earlier (design found under leaves).
Get STAINED GLASS 7.
Go to ROOM 24 (church).

ROOM 24
Actions:
Put completed STAINED GLASS into window. Then put MIRROR on pedestal, and turn it to face right.
Go to ROOM 38.

ROOM 38
Actions:
Beam of light from mirror reveals GREEN STONE on wall.
Go to ROOM 1.

ROOM 1
Actions:
Drag tile under lever out of the way, to reveal green space. Put GREEN STONE there.
Pull lever.
Drag six other tiles out of the way, to reveal dead боди of doctor. Click it.
Leave the room in any direction.
YOU WIN!!!