90% of the games I play fall into one of two categories: "PC Games from the 90s", and "Nintendo".
PC Games:The Obvious Game That Everyone Else Has Already MentionedX-COM: UFO Defense: Just started replaying this last week! And I also think TFTD is pretty darn awesome, but it has a few things weighing it down, unfortunately...
Warlords II: I haven't played this in a while, but I have good memories of it. I should go dig it out again...
Civilization: Classic...!
Commander Keen 4, 5, and 6: "CK6" was probably my favorite game when I was 10 or so. I could hum the music all day!
Betrayal at Krondor: I haven't played this in about five years now... I keep trying to find somewhere where I can download it, but no matter what I do I can't get it to work at all... It's VERY frustrating.
Masters of Magic: A very very very amazing world-conquest game!
Nintendo:Legend of Zelda: All of the games are fantastic, but my favorites are (in no particular order): "Ocarina of Time", "Minish Cap", "Majora's Mask", and "Skyward Sword". "OoT" is by far the most nostalgic game on my list.
Star Fox: "Star Fox 64" and "Star Fox: Command" were both incredible games. "Star Fox: Assault" was pretty darn disappointing.
Banjo-Kazooie: Definitely falls under the "Quirky" category. A practically perfect game!
Okami: This game took my breath away. If you've played it, you know exactly what I mean.
Diddy-Kong Racing: Definitely the funnest racing game I've ever played!
Pokemon: I was born in the early 90s. Pokemon was born in the late 90s. Perfect fit.
Pokemon Mystery Dungeon: I'm a little bit embarrassed by this one... The game is really aimed toward a much younger audience, and thus the story is amazingly cheesy, but once you get past that, it's really one of the funnest handheld games I've ever played.
Phew, that was a long list... Now if you'll excuse me, I have a few Chryssalids to take care of...