JMS recently announced that Marvel Comics is entrusting The Amazing Spider Man to him. According at a post by him in rec.arts.sf.tv.babylon5.moderated the first JMS written issues should be out in March or April of 2001.
He is also working on a new television series to be shown on Showtime, it will be in the sci-fi genre, but it won't be in the Babylon 5 universe. At the time of this writing, the show is in the early planning stages, with a pilot expected in early 2001. The show will be based on the european comic Jeremiah.
Finally, he has a script for a Rising Stars movie is in the works, but that project is also in the early stages.