So I just finished the game and love it - but there is at least one combination I haven't found so I thought I'd post the two I did find (read: the obvious ones) and hope to get help with the one(s) I didn't.
- Sam's Locker (Sam's Room): 0501 Found through picking up her note about secret panels -> searching all of the panels to get the combination (required for progression)
- Terrance's Filing Cabinet (Study): 0451 Found written on the folder in the corner of the library where you find a note from his editor.
- Safe (next to the servant's quarters): 1963 Found written on the wall right near the safe.
If you could post the clues or combination safes you found that I didn't, that'd be great - especially as you can keep exploring the house after the end.
Update: Figured the safe one out.