I really like both Hyrule Warriors games.  I'm still playing through Age of Calamity, so I don't think I can choose between the two yet, but those are my favorites.  I'm also pretty fond of Punch Out on the Wii.

Hotel Dusk, Last Window, Another Code and Another Code R in collaboration with CING. Nintendo has never made a game with these kind of stories and "mature" characters, so I'd say this collaboration produced something very unique for Nintendo fans during the NDS era. It's a shame that CING went bankrupt right after the launch of Last Window. I really miss their games...

The Legend of Zelda: Minish Cap in collaboration with Capcom would be another favourite of mine. Among the Zelda games that Capcom developed, I think Minish Cap is the best one. Easily one of the best games on the GBA and a truly unique Zelda adventure. This one deserves a remake in the same vein as Link's Awakening...

I personally don't count it as Nintendo owned a significant share of Rare at the time, but you're free to disagree as what constitutes a third party collaboration is often a blurry line.

Ok, I understand, I didn't know Nintendo owned a big share of Rare. So maybe Mario Party counts? I have to say that bumper balls, shy guy says, mushroom mix up and many other will for ever bring me good memories.