If you copy over files from X:\Users\<user>\Appdata\ relating to your programs you can preserve most settings. Works great for things like Firefox, Firezilla, Xfire. Almost everything.
They still require you to re-install teh apps. T here's no way around this. (Steam is a good exception though, you can just run the EXE, enter an e-mailed security key and voila, it's like nothing happened.
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