Nostalgia hasn't always bore out when I have gone back to play them again, but my fondest memories on PC gaming would be with the following games:
Space Quest 3 - Pretty much the first game I played on a PC, other than maybe Civilization
Civilization - See above ... Although I only played it once and couldn't figure out how to change the production in the original city.
Doom 2 - The first game I got on our family Pentium 60 (Before that I had an 8088 in my room, but I actually wrote all of my own games for that using BASIC, since it wasn't powerful enough to play very many games.)
Command and Conquer - I started playing Warcraft 2, and while fun it was nothing compared to the fun I had playing C&C. That game was a blast.
Mech Warrior 2 - I enjoyed the game Battletech, but rarely got to actually play it, and this game did a good job of simulating the rules for that game. Plus it has the best opening cut scene I had ever seen, and still holds up today.
Syndicate - I played through levels on this game over and over again, trying to complete the objectives in many different ways. My favorite was winning a level without ever being seen (by using disguises and bombs).