I assume by "JBoss 3.1" that you meant "JBoss Tools 3.1".
For the JBoss server, which projects are associated with it? You can find out expanding the server in the Server View (click on the triangle in front of the server name) - all associated projects will show up underneath the server. All of the associated projects will be deployed, if you don't want them deployed, remove the association (right-click the server and choose Add and Remove)