Yeah GX still looks phenomenal due to clever use of relatively inexpensive techniques and a blistering framerate.

Super Mario Sunshine still looks gorgeous almost 25 years later.

Possibly a controversial take, but I feel like the Gamecube has weirdly aged better than the Xbox.

Xbox was more powerful, and games like Chronicles of Riddick, Doom 3, and Halo 2 were seriously impressive at the time, but in retrospect I feel like their early use of pixel shaders hasn't aged as gracefully as Gamecube's best looking titles.

I think I know where you're going with this - and yes, Metroid Prime aged better than any of titles you mentioned ;)

OT: Apart from cell shaded games (that age particularly well), I'll go with RE1 Remake - kinda cheating, since most of the game is prerendered, but technically it is a 3D game.

Prime 1 and 2 are good examples, but I was also thinking of stuff like say Starfox Adventures or even RE4.

They just have a cleaner look to them that I prefer:

Excluding cel shaded and prerendered:

Mario Sunshine, RE4 (GameCube), Riddick, Doom 3, Chaos Theory (Xbox), DOA3, NFS Hot Pursuit 2 (PS2), MGS2, GT3, Enthusia, Forza, Tekken 5, and I'm going to mention ZoE2 again for the sublime particle effects and destruction; its use of cel shading is minimal compared to the other examples anyway.

Yeah - back then I would definitely pick Riddick as having way more "wow" factor with all the advanced tech, but that sort of game ages fairly quickly with new GPUs and new tech, so I'd say something like Fable on OG XBOX aged better. 

Yeah same, in the 2000s I would have said Doom 3, Halo 2, and Riddick were near the top of the pile for Xbox, now I'd favour more the likes of Panzer Dragoon Orta, Dead or Alive, Ninja Gaiden, or Conker. 

Aside from the ones listed before, I feel that RE4 has aged incredibly well for a "realistic"-style game. They did a phenomenal job on the OG on the GameCube.

Anything stylised. Wind Waker, Sly Cooper, Jak, Mario.

For more realistic looking games Gran Turismo 4, SSX 3.