Chrono Cross, some of the best graphics and aesthetics the PS1 had to offer, as well as Legend of Dragoon. Paper Mario for the N64 looked alright, but I guess it isn't hard to make that art style look good. Half-Life, Half-Life, Half-Life. Starcraft was pretty sweet too.
Going back to the 8- and 16-bit eras, Mario ALWAYS looked good. The Sonic games were alright, but 3 had more polish than the others. Ninja Gaiden, Kirby, Contra, Final Fantasy VI, Chrono Trigger, Terranigma, Seiken Densetsu 3 (Legend of Mana 3, never officially released State-side), the list goes on.
Honestly, I think the SNES games that DON'T look good would make for a far shorter list.