Speaking with Joystiq in an email exchange, The Binding of Isaac creator Edmund McMillen says that the upcoming Wrath of the Lamb download content planned for the PC version would be included in the 3DS game, and are waiting on Nintendo to approve it.
Ed says the project is moving forward, and hopes the religious aspects of the game won't be a problem.
The only news I have on the 3DS is that it seems possible but it's still going through higher ups to make sure there won't be an issue with the 'religious' aspect.
The planned DLC for the PC version contains "about 50 per cent more content" than the original game, which Ed says will be the only additional content he makes, since everything that can be done with Isaac will have been done.
McMillen also states that if the 3DS version doesn't come to fruition, then there are other possibilities, which likely include putting the game on digital download services such as PSN and XBLA.
Hopefully Nintendo won't stand in the way of a 3DS version of The Binding of Isaac.