I'm not an AS specialist but before someone more competent chimes in I'd suggest you take a look in the following plugins:
You might want to join the #jbosstools channel on irc.freenode.net and address your question to rawbdor or adietish.
Yes, Koen is correct about that being where to look for how the server adapters are defined.
But I don't think a new server adapter is needed - the version range check for AS 6 just needs to be opened up to allow 6.x instead of 6.0.x.
Your last error about NoClassDefFoundError is most likely caused by missing quotes.
Thanks Koen & Max, I'll have a look into it and see if I can get it working.
For anyone else reading this thread, Wolfgang Knauf has created a plugin for Eclipse Web Tools Platform which adds support for JBoss AS 6.1.
You can get it from his site here: http://www.cs.hs-rm.de/~knauf/public/
Note, you can use JBoss Tools server adapters for AS 6.1.x by adding the missing argument to the server startup parameters.