It's really difficult to say what is the greatest PC game of all time, since there have been many extremely good games through time...
So, i will name them by genre:
RPG: Baldur's Gate II/Fallout 2 (tied). Actually anything made by Bioware and Black Isle back in the day
RTS: The first Company of Heroes, the pinnacle of RTS gaming. Starcraft is so overrated. The new Company of Heroes sucks also...
Turn Based Strategy: XCOM Enemy Uknown(1993, not the crappy remake)/ Jagged Alliance 2. also tied for first place.
FPS: Crysis. The first, the rest are crap. It didn't have only amazing graphics, it had good gameplay too. Plus the multiplayer was good, but nobody played it because its hardware requirements were steep at the time of release.
Third person shooter: Max Payne. The first, although the second was nice too, the first is an example of how to do a noir game right...
Adventure: Now this is a difficult category, so i will go with the popular choice, Grim Fandango
Action Adventure: Assasin's Creed II. By far the best Creed game, with an incredible presentation and attention to detail. A wonderful game. Too bad all the sequels are crap...