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Well, in my past experience the main problem has been with GUI's, as they have a tendency to break across platforms. I haven't had an instance where, say, "Hello World" would break.
You need to tell me how you know they're "broken". It may be that the class files aren't broken, but that it's a misconfiguration and WebLogic doesn't see what you think it's seeing. If, for instance, you move JAR files to the wrong directory, but running an Ant script to recompile puts them in the correct directory.
You'll need to explain what "didn't work" actually means.
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