There is no real difference that I'm aware of.
There should be an uninstall program in the 9.1 install directory. If not -- no problem. Just make sure it isn't running (run jps and look for PELaunch) and then wipe out the files.
Or you can just leave the files where they are and ignore them. Both GlassFish and SJSAS are completely stand-alone programs -- i.e. no registry entries are created etc.
[Message sent by forum member 'bnevins' (bnevins)]
http://forums.java.net/jive/thread.jspa?messageID=244921