N64 by far. I agree the N64 didn't age well, but I had way more fun with it. My age at the N64 (13+) playes a big part in it of course, compared to my age with the Wii (23+).
Zelda OoT still feels as the best game ever. None other Zelda game since then came even close.
Goldeneye's singleplayer and multiplayer were really fun. Back then you still played with friends in the same room ;)
Perfect Dark looked so beautifull the first time I played it and the extra missions were just a game by itself. Multiplayer was really good.
ISS 98 Probably the game I played most in my life.
F-Zero Could play that game again and again. The steps in difficult level were really good.
Wave Race, Almost as good as F-Zero
Starfox 64 Again a game which I could play again and again.
The Star wars roque squadron games. Loved those
I played paper mario years later, but that one was really fun as well. Although it was my first and only paper mario as Zelda OoT was my first Zelda.
Besides these games I still played at least 10 more which were at least an 8 for me.
Mario Galaxy 1. Best Mario Ever. Liked it a lot more than Mario64
Resident Evil 4 Extremely good, and the controls (after i got used to it) worked really well.
Didn't play Xenoblade. But I guess this is the list I have really good memories of for the Wii ;)