Star Wars: Republic Commando (apparently there IS an in progress fan-made remaster, but I've never so much as seen it or know what the name is)
Emperor's Battle for Dune: this game needs new graphics and better controls, unit balance, and story. Basically a new game built off what already exists. It will never happen, but it would be cool if it did.
Various Zelda games
A few Twisted Metal games (I grew up with one of the PS2 ones)
Dungeon Keeper 2 (War for the Overworld exists. I have it. I like it. But it's not the same. I'd like both on my modern rigs)
Honorable mention: Rise of Legends. I say this as an honorable mention only because the game is perfectly playable as it stands even in 2021. Its in game graphics are just meh and the cutscenes... oh god, they're bad (other than the beautiful opening cinematic that is). I really wish this game had a lot longer story/campaign.