I can think of only two possibilities.
1) Write a sript that deploys/undeploys the applications (such that only the desired application is deployed) and starts JBoss.
2) Clone the configuration you are using and deploy individual applications to each clone. For example, for myapp1.ear, copy server/default as server/myapp1 and deploy myapp1.ear to server/myapp1/deploy. Then when you want to run only myapp1, enter: ren -c myapp1. (You could also write a script to do this each time you want to run an app. That is pretty much what I do.)
I just noticed that this is the deployer developer's forums (didn't pay enough attention when the I got the notification email). I also noticed that you posted this same question to multiple forums.
1) Do not post user questions to the developer forums!
2) Do no post the same question in multiple forums!
(Could someone move this post to a more appropriate forum?)