I'd love to see a Mario and Luigi cooperative platformer...
Whatever it is, it needs to make use of the controller. I think Jungle Beat could be a great killer app, it just needs about twice as many levels to appease critics. Maybe it could use a dual-remote drumming setup, although that would mean Nintendo needs to include the second controller with the game or the system. For that matter Nintendo could probably think up some more creative way of using the remote to play the game, while still making it physical like Jungle Beat was.
I think a new Mario platformer could do just fine too, though. While there have been hints that Nintendo is having trouble finding a direction for Mario 128, it's pretty late in the game to be starting up a brand-new title to act as the "killer app". Ideally the real killer app is already well into development.