If you're going to maintain 2 versions, then I'd rather put the GWT-specific one in the super-source path, so that GWT will use it while the server will use the other one; they both have the same name and package so your code that uses them is "portable". (if you don't know what super-source is, it's what GWT uses to emulate classes from the Java Runtime, and you can take advantage of it too; see http://code.google.com/webtoolkit/doc/latest/DevGuideOrganizingProjects.html#DevGuideModuleXml )
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