I don't know if this is too late, but I thought I'd throw in my own list. This is just the games that really stick out for me as being amazing and/or a lot of fun. I'm going to try to avoid as many of the big names (Doom, etc.) as possible, as they've already been mentioned.
1. Ultima Underworld/Underworld 2 - Staggeringly advanced FPS/RPG hybrid.
2. Syndicate - Violent, cathartic, dark, and utterly brilliant.
3. Rockstar - Wizard's hilarious text-based rock star sim almost defies description. Funny and clever.
4. Star Control 2 - Perhaps the most beautifully written game ever created.
5. Commander Keen (1-6) - Nintendo had Mario. We had Commander Keen. I preferred the latter.
6. Moraff's Blast - A psychedelic re-imagining of 'Breakout'. Hours wasted.
7. Space Hulk - Games Workshop comes to life, with a dash of 'Aliens'. Tense, nerve wracking stuff.
8. Flashback - Still, in my opinion, the greatest platform game ever made. Delphine's masterpiece.
9. ZZT - Epic's level creator and scripting language took years of my childhood away from me. Wouldn't have had it any other way.
10. Carmageddon - Pure fun alchemised into binary.