Damn. Too many to talk about. Anyone ever play Total Annihilation, though? It was an RTS from the late 90's, Supreme Commander was sort of its 'spiritual successor.' That was the FIRST PC game I ever played, I was probably 9 or 10 years old. Shit, it was so good. Dunno if it holds up today but it got my into PC gaming as a little kid and more specifically the RTS genre, so I thought I'd mention it.
If I had to list my top 10 off the top of my head right now, though, without doing any musing at all, it'd go something like (in no particular order):
1) Deus Ex (On my gaming Mount Rushmore, easily)
2) Mass Effect (series, see below)
3) Warcraft 3 (my favorite RTS ever, hands down, fantastic campaign, story and world, and incredibly fun multiplayer)
4) Half Life (again, gaming Mount Rushmore and all that)
5) Knights of the Old Republic (possibly my favorite RPG ever)
6) World of Warcraft (see below)
7) Metal Gear Solid 3: Snake Eater (peak of the series, although MGS5 is close)
8) Grand Theft Auto 5 (almost too new to include but having just finished it this past summer, I was just blown away)
9) Halo (I've owned every game in the series, multiplayer hit its peak in Halo 2 but I'll stick with the original just for its iconic nature)
10) The Legend of Zelda: Ocarina of Time (do I need to say anything?)
I know I cheated by listing the whole Mass Effect series, fuck off. Ending aside I thought it was a phenomenal feat in video game storytelling and will forever be one of my favorite gaming experiences of all time. I also know I included WoW on that list. I'm a huge Blizzard and Warcraft fan, and my friends kind of got me into WoW back in the day and I've played it on and off since (although never hardcore). The times on there with my buddies are some of the most fun I've had on a video game, ever, so it'd be dumb for me not to include it even though only part of that fun came from the game itself.
Deus Ex for a long ass time was my favorite game of all time. I think it still is, but I'm afraid to go back and play it and have it totally ruin my vibe. I haven't played the newer one, but I think I'll give Mankind Divided a whirl. Deus Ex: Invisible War just left a bad taste.
Lots of older, iconic games that deserve honorable mention, but just haven't aged very well: Goldeneye, for example. I logged a shit load of hours on the split screen with my friend back in the day, and that really began the age of console FPS for me. Perfect Dark was a nice followup for Rare, too. Mario 64 and Majora's Mask were some other favorites on N64.
That's a rough listing, if I actually sat down for an hour or two and thought about it I might switch it up a bit and change things out.