I don't really agree that Ocarina of Time has aged well. It still has that raw fun element to it, but its very unrefined compared to its follow-ups, and it doesn't have the sheer sense of wonder it had on release. I have the same opinion of Mario 64 and Final Fantasy VII (fuck you, I like turn based combat). Res Evil has aged terribly as well. I don't think any of the verb based point and click adventure games come across well nowadays either, but that may just be because it utilises such archaic gameplay elements (still a good experience though).
Metal Gear Solid I think has aged very well. The heavily stylised characters go some way towards helping that, and the enclosed environments aren't too restrictive.
I agree with the person who mentioned the Thief series still being very fun too. I recently played The Dark Project for the first time, and after getting used to it, I found it a very enjoyable experience. Horrific graphics and animations, but it was engrossing enough for me to mostly overlook that.
I was very suprised how well Nights comes across today. Sure, the graphical limitations of the Saturn are there for all to see, but such fluid gameplay, bright, vibrant backgrounds and warped character designs are timeless.
I could go on, but thats all I'm saying for now.