https://www.youtube.com/watch?v=9V_CNry0KyE

It's 3D...

Definitely Wind Waker! I would also say that Conker has aged pretty well for a N64 game!

The first one posted was U-Mos, sentinel of the Luminoth.

In case anyone forgot about them: Wind Waker, Mario Sunshine and Star Fox Adventures.

Also, I would add Majora's Mask, Silent Hill 2, Final Fantasy IX, Vagrant Story, Banjo Kazooie, Smash Bros Melee and both Pikmin games.

3D games started to look good with 6th gen...it's much harder finding 5th gen titles that hold up under much scrutiny. I'm ~okay~ with how FF8 looks, but FF7 has aged so poorly its unbelievable.

Final Fantasy IX is another good one.. it's pretty impressive how well that game holds up compared to VII and VIII!

Beyond Good & Evil and The Simpsons: Hit and Run.

Silent Hill 2 and 3 still look amazing.

5th sentinal of the luminoth, son of V-Mos, the third sentinal of the Luminoth. 

Like many have already mentioned, most GC games still hold up today like Rogue Squadron 2 & 3, Melee, Pikmin 1 & 2, Prime 1 & 2, Sunshine, Star Fox Adventures, Wind Waker, F-Zero GX, RE4, etc. It's an even bigger testament to the console that a good chunk of the games I just listed were either launch titles or released within the first year of the console's life.

Xbox also had some beauties like Halo 1 & 2, Panzer Dragoon Orta, Crimson Skies, Ninja Gaiden, and Riddick Escape From Butcher Bay. There's only a few PS2 games that I would say hold up visually more for their art direction such as Shadow of the Colossus and Okami.

Before 6th gen 3D games get alot rougher around the edges (literally), but some standouts are still Rare games like BK 1 & 2, Perfect Dark and Conker on N64, and even Panzer Dragoon Saga on THE Saturn holds up pretty well. Beyond the 5th gen I'd say only Star Fox holds up today.