Imo Deus Ex is still stands very well on the graphical front, even without HD mods etc.

..... Okay, those are all games made after 2001 minus Silent Hill 2, what do you define as old then?

Depends on your graphic expectations. I'd say Prince of Persia from 1990/1991 still ages well now. But that's just me.

WoW and Warcraft 3

Well system shock 2 and startopia for starters

SS2 patched to 1080p looks great still, Sure would be nice to get a Extreme HD texture pack like the fallout games but it still looks great never the less

Pro pinball series, Thats cheating i guess :P

The armored core games on the PS2 still look great

I cant really think of anything at the moment, I dont know what is too late for something to be classed as a old game,

Legend of Zelda Wind Waker

The Last Express

Daggerfall

Final Fantasy 6
Legend of Zelda: Wind Waker
Final Fantasy 10
Metal Gear Solid 2: Sons of Liberty

...can't think of anything else at the moment.

Grim Fandango
Blade Runner

Freespace 2 still looks pretty

Dawn of War
Rollercoaster Tycoon
Rise of Legends
Rise of Nations

I second Final Fantasy 6, the sprites in that game were gorgeous. Same goes for Chrono Trigger and a lot of the other SNES-era RPGs. I'd also add (controversially, I think) Super Mario RPG. I loved that game, graphics and all, and still do.

Beneath a Steel Sky and Broken Sword are lovely, as are a lot of other adventure games. That aesthetic just really appeals to me.

Any 2D sprite game, those things are timeless.