I also love Nuts & Bolts, though I think it would have been better as a spinoff game starring Tiptup. I mean it would make so much sense for a game about a turtle to require vehicle in order to move fast. Also Trophy Thomas should have been a rabbit.
Anyway, my favorite Rare games are (in no particular order)...
All Donkey Kong games
All Banjo-Kazooie games
All Conker games
Diddy Kong Racing
Jet Force Gemini
Grabbed by the Ghoulies
Star Fox Adventures
Sabre Wulf (on Gameboy Advance)
Basically I absolutely adore any Rare game that features exploration as an element of the gameplay. Also, I'm a pretty big fan of Killer Instinct Gold and both Viva Pinata games as well, though not quite as much as the above.