Prince of Persia from 1989 has stood up to time better than anything else I can think of.

2D VGA & later usually look at least acceptable, SVGA usually look good (as long as the game itself is not an artistic abomination). Earlier needs to be judged on a case to case basis.
3D: If you use polygons then post 94 in terms of metallic and other non-organic things (cities, space ships and so on), and post 98 when it comes to living creatures.
For "3D" games with sprite-based objects, that is a lot harder to tell. Doom still look quite alright, but Might & Magic 6 looks horrible.

I think the original StarCraft has aged pretty well. It's helped greatly by a very decent aesthetic, but I honestly think it looks better 14 years on than the sequel does two years on. Yes, it's not as shiny, but it has a... darkness and a grime to it that I really like.

In terms of 3D games, both Jet Set Radio games will, I think, be timeless.

Age of Empires 2 looks beautiful in 1600x900.

I'm with a lot of other folks in saying that most 16-bit looks good today as a rule, and there are definitely some great 8-bit arts as well. It's the wobbly areas like transitional 3D, early Game Boy games, and early PC games that need the stand-outs pointed out, and I am really not the best person to do that.

While it's pretty much soundly out of the early GB period, I do want to give a little shout-out to Link's Awakening, one of my personal favourite games, which had graphics so nice for the system in 1993 that the GBC Zeldas just snapped them back up in 2001.

Gabriel Knight 1 : Nice pixel art that does not make my eyes bleed.

Baldur`s Gate 2: I sometimes still stop when I`m playing and just stare at the screen, admiring the careful detail that went into creating the environment. It can look dated on lower resolutions and/or fullscreen mode though.

Heroes of Might and Magic 3: It just simply does not seem to age at all due to the very nicely detailed 2D art, especially in the case of unit models and town backgrounds.

I've replayed Homeworld expecting to have to forgive dated graphics. It was absolutely gorgeous.

Not extremely old, though.

anything isometric

Dude I know its your opinion but GTA 3 looks ugly.

Vice City though still ugly has beautiful lighting and San Andreas as better Car models for the time.

TBH Vice City had even worse graphics than GTA 3 and the lighting made it worse.GTA 3 atleast was a first in the genre and the dark styled Liberty City looked preety cool.

Unreal Gold. :)

Relatively nice textures and water surface animations, nice skies and ambient lights. The polygons might not look so good today, but I think the "wrapping" is still pretty nice.

And I see no one mentioned Soul Reaver...

Shogo Mobile Armor Division. Oh LAWDY I remember this looking MUCH different... Still an absolute blast to play, and you can probably finish the game in an afternoon, but wow those graphics have aged!

Software rendered Quake 1 still looks good to me. The maps are beautiful if limited in palette and the enemies look like living papercraft. The animation looks interesting because it was all done by hand and without the use of bones/ armatures (it's like exaggerated claymation).

http://en.wikipedia.org/wiki/Papercraft