Ewwww wow, I thought Doom 3 was butt-ugly when it came out, forget now.
Easily the game that's aged the best for me where 3D graphics are concerned (ok ok, so it's kinda cheating) is Resident Evil on the Gamecube. That game looked phenominal back then and still looks really REALLY good now. In terms of visual coherency it looks much better than 99% of things that come out now, and was probably the best set of graphics to ever grace standard definition. With Ninja Gaiden on original Xbox coming a close second.
In terms of 2D graphics I think a lot of games have aged incredibly well, old Zelda games, old Mario games, Contra 3 looks incredible still, so does Super Metroid, etc. A lot of the classic 2D SNES-era games still look amazing now imo.