1. StarCraft. I dont remember if I played Command & Conquer or WarCraft first, but I know I preferred WC. Then WCII came along, and it was also very good. But StarCraft, far from being simply the WarCraft in Space that many originally expected it to be, was simply on another level. In terms of gameplay, the 3 utterly unique yet balanced factions, the powerful map editor, and the level of support that Blizzard has provided has made it the best RTS Ive ever played. But its actually the lore, setting, and characters of the SC universe that truly pushed it above and beyond all other PC games for me - Raynor, Kerrigan, and Tassadar are some of my favorite gaming characters ever, and for that game to be a RTS is something I almost never wouldve believed.
2. Civilization II. Im still not sure if I could definitively consider II or IV to be the pinnacle of the Civilization series, but one of them has to be on the list. And maybe its just a case of nostalgia, but I think I would tilt ever so slightly to II. The original Civ was an amazing game for its day, but Civ II was a massive improvement upon it in almost every way. It looked better, it sounded better, it was deeper, the AI was better (yes, AI in Civ has always been... quirky, shall we say, but this *was* 1996), and it truly became the game that kept you up deep into the night thinking just one more turn.
3. Portal. The Orange Box was a pretty momentous release, but the focus and the hype were, understandably, on the next installment of one of the most critically acclaimed PC games of all time and a multiplayer focused FPS followup over a decade in the making. Portal, on the other hand, was regarded by most as the bonus free game then. Yet the basic concept of the game captured my attention from the first time I read about it, and it actually became the main reason for my purchase of The Orange Box (I actually still have not played HL2 Ep 2 due to waiting on Valve to release Ep 3... sometime, and I never was a big MP FPS fan so didnt play much TF2 either). And boy, it did not disappoint. The gameplay mechanics were fun, the puzzles were creative, the characters (OK, just one character really, though the WCC arguably could count as one!) were captivating, and the now-famous (or would it be infamous?) ending credits/ending theme is the best Ive seen in a game in years. All in one damned-near perfectly paced package - truly the most brilliant game of this generation.
4. Prince of Persia: The Sands of Time. I think I might have played the original PoP at some point, but I certainly didn't have any attachment to it. And I also tried the absolutely atrocious PoP 3D, which obviously didn't endear me to the series either. But in just a few short hours, Sands of Time has made me such a fan that I've bought every single subsequent game in the franchise. Sure, the combat was simple and rather repetitive, and some platforming bits were tedious thanks to the camera angle. But the time rewind mechanic, the eminently like-able prince and Farah and the banter between them, and the brilliant way the story was narrated, all came together to make a game that truly defined the action-platformer, maybe even to this day. And on the PC platform especially, where there have been far fewer high-profile 3rd person action games, it really stands alone.
5. SimCity 2000. SimCity created the modern city building game and was quite revolutionary. Then SimCity 2000 made it damned near perfect, and still stands as the pinnacle of the series and genre. Yeah, laying water pipes is quite annoying, and late-game is basically just build as many arcologies as possible. But the core of the gameplay mechanics are solid, and the fact that you could play the game indefinitely without a win condition was brilliant fun.
6. Star Wars: TIE Fighter. There are a lot of great space sims, and the Wing Commander games are probably more important in the genre, but for me this is the one that still stands above them all. Yeah, a lot of that is because its a Star Wars game, but I can hardly hold that against it, because it does such a fantastic job in making the most of the franchise. Taking the perspective of the opposing side was a brilliant move, and I would say that this is still the best Star Wars game set in the Rebellion era.
7. Star Wars: Knights of the Old Republic. If I had been told in 2000 that an RPG set in the Star Wars universe may become arguably the best Star Wars game ever made, I'd have laughed. But KotOR delivered almost everything I could have ever wanted out of a Star Wars RPG, and in spectacular fashion. Yes, the fact that it came after the release of the divisive first 2 movies of the prequel trilogy probably helped perceptions (certainly there were plenty of proclamations of it being a better Star Wars than them), but the game is absolutely solid on it's own. The story, setting, and characters are all very well done (HK-47 is one of the most memorable characters in a videogame ever), and the gameplay felt fast-paced and action-oriented enough despite, at it's core, still being a D&D roll-based system.
8. Transport Tycoon. Sid Meier may be the best strategy game designer ever, but Chris Sawyer is truly the master of the tycoon game genre. Railroad Tycoon is good, but Transport Tycoon is brilliant, and the later RollerCoaster Tycoon series just fully cemented it.
9. Half-Life 2. The original Half-Life was probably the first FPS to do story properly, but HL2 really took it to new heights. The narrative is well delivered, the characters are well rounded (and gets bonus points for Alyx being one of the best female characters in gaming), the levels are interesting, and the Gravity Gun is just plain cool. Honestly, about the only thing I can say bad about HL2 would be that for as good as it is, a surprising spin-off in Portal just ended up being that much better.
10. Baldurs Gate 2. There are not enough words I can write to properly describe a game of this epic proportions. But the fact that a decade later it's still considered the definitive fantasy/D&D RPG really says it all. I still prefer KotOR when it comes to WRPGs, but Ill readily admit that the only real reason I have that above BG2 is my affection for the Star Wars universe.
And the barely-missed-top-10 honorable mentions:
Deus Ex
Heroes of Might and Magic III
Planescape: Torment
RollerCoaster Tycoon
Star Wars: Jedi Knight: Dark Forces II
System Shock 2
Tribes 2
Worms 2