Far too many...
My most recently discovered would be The Ur-Quan Masters. A GPL-port of the 3DO-port of the DOS-based Star Control II.
For PC games, mostly some select HL mods. Natural Selection, BrainBread, TFC, The Specialists, and of course, ESF. Most of the Blizzard games: StarCraft, Warcraft II, and Diablo I/II. Microsoft's Freelancer and Starlancer rank up there for me as well.
For console games, not many outside of the range of classic SNES and few N64 titles. (I was a Nintendo guy when I played console games, but I don't play them much anymore.) EarthBound, Chrono Trigger, Final Fantasy II(IV) & III(VI), Zelda III (A Link to the Past), Illusion of Gaia, Harvest Moon, The Legend of Zelda: Ocarina of Time, and Banjo Kazooie (don't you judge me).
I'm sure I'm forgetting many, too.