Great thread!
Super Metroid will probably always be my favorite Metroid (and game), but Metroid Prime comes at a close second. The first Metroid certainly deserves an honorable mention, as it created a genre/mood that few games have managed to emulate, let alone best.
I think it might be fun to do a "worst Metroid" thread as well. Certainly the Other M backlash is strong, but I'd be curious to see where the others would end up.