JBoss is by no means a dead project; it is very active and has strong commercial backing from RedHat. They spent a significant amount of time redesigning the entire app server to run off the new JBoss Microcontainer. Not sure if it was worth the 3+ year effort but the release notes are here:
http://sourceforge.net/project/shownotes.php?release_id=645033&group_id=22866
As with any big rewrite of an app server, I would tread carefully on JBoss 5. If you are programming simply to Java EE specs then Glassfish will probably suit your needs fine. If you want to use parts of the JBoss stack (Seam, JBoss AOP, etc) then it might be worth targeting either JBoss 4 instead of 5 depending on your QA / deployment timeline. By the time 5.1 comes out, the major bugs should be fixed and you should hopefully be able to migrate easily then.