AceBandage
Banned
http://www.shacknews.com/article/71781/the-binding-of-isaac-awaiting-3ds-approval
Speaking on Formspring (via Joystiq), McMillen said that "a publisher I know is currently asking Nintendo if they would be OK with Isaac on the 3DS." Should Nintendo approve the game, the publisher will then begin the porting process.
Unfortunately, if Nintendo doesn't approve the port, it's unlikely we'll ever see Isaac escape to consoles and other platforms. McMillen notes that 3DS is "the only other system you might ever see Isaac on," showing his continued dedication to Nintendo--in spite of never being able to release Super Meat Boy on WiiWare like originally intended.