I'd say most games that were good in the day have aged pretty well. If they're still playable on a purely non-cosmetic level, then they have indeed aged well imo.
Judging by graphics alone, both 3D as well as 2D ones look good, although the 2D ones tend to get more attention, probably because they were a few generations ahead of the 3D ones if you compare them on their respective timelines. Games like Valkyrie Profile and Cv:SotN look especially great imo.
However, I for one, happen to like the "boxy/blocky" and pixely 3D-models of the PS1 era and I actually think they kind of have a retro feel to them. Makes me all warm inside.
There are, however, those that stand out more than others. Square games, especially FF8/FF9, Chrono Cross and Vagrant Story tend to get my attention graphically because some of the special effects still are top notch, lighting effects in particular. All those summons may be tedious in the long run, but most of them look absolutely stunning. The same can be said about magic and special attacks.