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What real-world projects would you suggest looking through the sources?
As I’m learning Java Swing, mucommander seems to be a decent example. The code is excessively commented though.
EDIT: No shameless plugs plz :).
Take a look at the Windows version of truecrypt. It is one of the best organized open source projects I’ve ever seen. You can almost tell how the whole thing works just from the directory and file layout.