Yes, there is indeed a Humble Bundle in cooperation with Nintendo. But it's region-locked. Here is the list of countries where it's available:
https://support.humblebundle.com/hc/en-us/articles/206177517
For minimum $1 you get:
Guacamelee! Super Trubo Championship Edition (Wii U)
Woah Dave! (3DS)
Mighty Switch Force (3DS)
beat the average (around $9 right now) to get also:
The Fall (Wii U)
OlliOlli (Wii U and 3DS)
Moon Chronicles (3DS)
Sportsball (Wii U)
Gunman Clive (3DS)
BIT.TRIP Presents...Runner 2: Future Legend of Rythm Alien (Wii U)
Pay $10 or more to get all of the above +
Stealth Inc 2 (Wii U)
Steam World Dig (Wii U and 3DS)