I was in early Act 2, and after picking up the key from the street thugs in the Gift I found the house it's supposed to unlock and went in. The game froze up on loading the interior of the house, and after leaving it for five minutes I finally took the option to force quit. When I started it up again, all my saved games were deleted! By chance I actually had my save folder (user/appdata/local/temp/obsidian entertainment/pillars of eternity/) open on the desktop after the crash, so I know they were there after the game locked up and closed -- but now, after opening the game again, that folder is empty except for a 1.7MB file called LoadedSave.zip. There goes 12 hours of progress....

Check C:\Users\USERNAME\Saved Games\Pillars of Eternity

Wish I'd seen this before fixing it so I could see what was in that folder. Something was up because when I tried to play the game the "Continue" and "Load Game" options were greyed out and unselectable in the main menu, exactly as if there were no accessible saves. I solved it by extracting the contents of LoadedSave.zip into the temp/ save folder. That restored all my saves.