1. Ultima 7 Parts 1 & 2
By far the most immersive "real world", real time RPG of its era. No other game had fully scripted behaviors for each NPC in the entire world, and they would react to changes in their environment as well. It defined real time RPGs, and pretty much paved the way for current MMORPGs as well.
2. Star Control 2
Where else can you get a very simple game with enthralling 2D shooter aspects, cool alien races, and THOUSANDS of star systems to explore all while upgrading your ship and having your captain enhance alien relations with the all female Syreen race?
3. Wing Commander (1 and 2)
Chris Roberts was a pioneer in the field. Not only did he produce a quality title and put Origin on the map with a space combat sim of epic proportion, but he also invented the "cinematic game". Wing Commander was probably one of the first successful commercial titles that used cut scenes the way it did and told a story that was top notch, worthy of just about any SciFi geek's movie library.
3. Civilization
Not much to be said other than Civ brought the board game to life on the computer.
4. F-19/F-117/F-18/Apache (Microprose)
Welcome to the grand daddies of combat flight sim. Microprose defined the genre.
5. Silent Service II
Wow. Just wow. Being a fan of war history, particularly WWII and the Pacific theater, Silent Service II was just plain awesome. The slow pace of trying to creep your way into a Japanese battle group without getting detected while understanding their normal evasive patterns so you can get a couple torpedo shots off at a carrier and hopefully cripple it before getting your ass handed to you made it intense. Then, on a macro scale you got to watch the war unfold before your eyes as you took down merchant ships and small Japanese naval ships along the way.
6. Planetside
MMOFPS. The one, the only (literally only, because there is no other true) MMOFPS out there.
7. Mass Effect 2
Out of all the games I've played, I keep coming back to this one. It's beautiful, the story is great and it plays like a cinematic masterpiece. I hate sitting in front of a TV watching a mind numbing show because I'm not doing anything. Playing ME2 is like being IN a movie.
8. SimCity 2000
This, in my opinion, is the first real city builder out there. Not only that, but it was an evil genius's toybox of destruction. Seriously... the only real reason to build your city was so you could unleash disaster after disaster upon it.
9. Unreal Tournament (pick one)
Quake deathmatches were fun, for a time. But Unreal Tournament just made FPS's fun. Green plasma beams of face melting death, thank you. And dm_morpheus was ever so much fun with the shock rifle. Sure you didn't get the kill... but you could rest satisfied that the dude you just shot won't be landing on anything except a respawn.
10. Mechwarrior 2
Rounding out my top ten, I'm gonna have to saw MW2. It was a FPS, plain and simple. A very SLOW FPS. With lots of guns. And robots. BIG fucking robots.