How to reenable Java Preferences
This is a partial answer and will need adding to, mainly to show the change in Info.plist and an official reference for it.

It seems (from this blog) that the structure or the Info.plist in running packaged Java apps has changed. The blog says in Mountain Lion but I would have the same issue in Lion, the issue is the change in Java. 

Thus I can see two ways of running pakaged apps


Install java 1.6 from Apple (running Mongo.app uses this one for me)
Repackage the app using the suggested AppBundler