Is this an application that you've written yourself? Or a commercial app?
Not that it matters, really. By their very nature, Java and Javascript have been designed to run in their own sandbox... and care has been taken to forbid them from interacting (ie - launching) with other apps (though, in true Microsoft fashion, they've circumvented this security feature in IE and provided the ActiveXObject... which can launch a limited set of applications - typically MS Office apps).
There are ways around it with Java... but, to be able to launch something on the client-side with Java, the user needs a true JRE running client-side as well.
Hope it helps,
-Carl