In general, 2D games tend to age much better than the N64/PS1-era 3D games have (just look at how great Symphony of the Night looks and plays next to a lot of the games from the same era), but I think that the first Silent Hill game is one of the rare 3D games that still looks and plays great. The clunkiness of the controls actually works in the favor of the game's story (of an Everyman grossly unprepared for the situation he has found himself in) and the graininess of the graphics (coupled with use of oppressive fog and darkness) adds to the mood, whereas most 3D games of the time look almost comically primitive today.
Speaking of primitive, I only recently played the original Doom for the first time (more out of curiosity and a sense of duty than anything else) and I was shocked at how much fun I had. The game has aged in exactly the right way; it looks and sounds ridiculous today, but gloriously so. It instantly makes me think of a bunch of burnt-out teenagers in metal T-shirts slumped in front of their monitors at 3am on a Saturday night, but in the best possible way.
I should add that I think most of the classic Nintendo franchises have aged incredibly well through the years, but I take it as a given that everyone else already thinks that.
