I'm gonna go with the sentiment that 3D Accelerated PC games are really the big ones that have aged well (especially those made in Quake and Unreal engines). And not just games from 1999. Quake, Hexen 2, Quake 2, Heretic 2, and Unreal were all 1998 or earlier. Quake 3 is almost cheating because it was released in Dec 1999.
N64 games have aged worse, but not as poorly as nearly every 3D PS1 game. Even with an emulator with a resolution boost and post processing, PS1 games just look like a mess.
Yes! In my list I forgot Heretic 2, if we don't consider later mods, that can make many games with scalable engines look good even for modern standards, see for example Morrowind, that was already really gorgeous, even compared to most of the other games using the Quake 2 engine. Unreal was gorgeous too, but it had the advantage of using a more recent engine. Heretic 2 OTOH achieved results as good using a tweaked Quake 2 engine, the first time I played it, it made my jaw drop even comparing it to Quake 2 that still was one of the best. It's use of lighting to create atmosphere is still one of the best I've ever seen.
Hexen 2 OTOH disappointed me a little bit, yep, IIRC it used a tweaked Quake 1, not 2, engine, but that wasn't the problem, I just think that while Heretic 2 changed the old Hexen/Heretic style for something both new and really great, Hexen 2 just didn't manage to make its new style great too.