A few 3D games indeed aged extraordinarily well IMO. Tobal No. 1 and Tobal 2 come to mind. Both still look incredible today thanks to stylized interlace gfx and smooth 60 fps. Also N2O by Tony Crowther (music from the Crystal Method) is 3D and aged extremelly well, because it is so polished and psychedelically timeless. R-Type Delta and G-Darius have aged very well. Again the stylized artsy design polygon gfx, psychedelich effects, and smoothness of gfx and gameplay matter here to make them still good by today's standards. Mr. Domino aged well too, again 60 fps and stylized polygons is what counts.
In terms of 2D I want to mention some more amazing gems. Adventures of Lomax is another breathtakingly beautfiful 2D game that aged incredibly well. In fact, its pixel artsy 2D gfx are miles ahead of any modern 2D game IMO (see attached screenshot). Heart of Darkness is also very very beautiful on Playstation (not so much on PC). Raiden DX aged very well. It has all these beautifully animated little particle effects and explosions that destroy things on the ground, smoldering little leaves on the ground etc. The Bubble Bobble style game Yoyo's Puzzle Park is an explosion of beautiful 2D effects and cutesy animations that also aged very very well. Each world is a new surprise with new effects and new enemies, including transparent water where each enemy releases air bubbles, lots of little animations in the backgrounds etc. Megaman 8 aged very well, too, for similar reasons as Yoyo's Puzzle Park. It has hundreds of little animated objects on screen at time, all beautifully drawn and animated.