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I have to admit I don't do Windows, so all I know about winMerge is what I just looked up on the internet.
If you are comparing source code or text files you might try FileMerge which is part of Xcode 3. Doesn't do folders but seems capable with text and source code.
One of the other Wrox authors uses it quite a bit in his book. It is not a part of Xcode 4 though.