I couldn't stand Metroid Prime. It's very repetitive. The entire concept of retracing your steps constantly and killing the same respawning enemies is really lame, IMO. They made a BAD FPS when they were trying not to make a FPS.
My favorite game for the system is definitely Eternal Darkness. It has a really cool concept and the story is quite good. Very atmospheric.
Other than that, I also like ExtremeG 3 and F-Zero GX. F-Zero is ridiculously hard though.
The Rogue Squadron games are pretty but very shallow. Star Wars Bounty Hunter is sorta cool-ish. Waverace Blue Whatever is a good followup to the N64 classic, with lots of improvements to gameplay.
Resident Evil 4 sounds like it's a gotta-get, but I haven't tried it yet.