I am not tremendously familiar with WebSphere but would love to hear how you make out with this. I have ThinApp'd other web applications.
You can use AppLink to link to a version of Java, but my suggestion would be to ThinApp it with Java first just to make sure you can get it working that way first.
Sean, VCP
http://www.vFAIL.net
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I
Sean
http://www.seancrookston.com
http://www.twitter.com/seancrookston