Intelligent Systems co. is a first party that design and distributes the official Nintendo dev kits and tools, including DS and GC tools. Many of these official Nintendo tools also exist for Mac OS. The actual Nintendo GameCube dev kit boxes are not PCs, they are custom boxes running a PowerPC and a Flipper GPU. Tools on PCs and Macs can be used to transfer data back and forth.

Nintendo's president, Mr. Iwata, delivered his last three keynotes standing behind his PowerBook/MacBook. Iwata quoted Steve Jobs at last year's E3 keynote, and said he admires him. Other Nintendo officials mentioned Apple a few times since then.

Shigeru Miyamoto is known to be a Mac user. I have a photo of him sitting at his desk at Nintendo and you can see a PowerMac there (It's an old photo I must admit)

Anyway I'm not trying to prove that there's a secret connection here, but certainly they share some of the same ideals.

The funny thing about the GameBoy Micro is that while it's obviously inspired by the iPod mini, the original iPod certainly was at least in part inspired by the GameBoy form factor, which itself may have been inspired by the original Macintosh shape :)

The important thing to remember is that Apple and Nintendo don't compete directly with one another, their markets don't overlap and are complementary. Apple now does most of what Microsoft and Sony do (Computers, OS, Music/Media distribution, consumer electronics) except games. On the other hand, Nintendo is focused on games and game consoles.

I think that the reason why nothing happens between Apple and Nintendo is that Steve Jobs didn't play enough Nintendo games in his life :)