Iwata re-programmed the entire game as a favor as well just to save the game from being canned essentially.

Super Mario RPG hands down. Dam it just give us a remake already! T_T

Great answers I see here. Would Metroid Prime count? Retro started development months prior to the acquisition, and the game was released 6 months later?

 Nintendo helped create the studio from former Iguana members (Turok) Nintendo helped found them in 1998.

Super Mario RPG managed the almost impossible task of making me, who hates turn-based combat, still consider it a great game, so for that alone it deserves special commendation.

Yea Iwata worked at Hal at the time but he also helped out Game Freak a few years later with Pokemon Red, Blue & Green despite still having to run Hal. The man was a machine!

Tokyo Mirage Sessions obviously

After doing some research, I just now found out that Nintendo SPD shared in the development of Fatal Frame 4, one of my favourite games of the last generation.

So that jumps pretty much straight to the top of my list, probably second only to Bayonetta 2, which again I'm not sure how much Nintendo was involved in that one beyond just funding/publishing.

Gonna go with Astral Chain on this one.

Does Goldeneye count? what about mario party games for the 64. they are all amazing and I spent countless hours playing them with friends and family.