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http://sourceforge.net/ is also a good place to start, most of them are free and open source. If you're using Ubuntu Linux then http://www.getdeb.net/ is a place to check out. On a debian Linux you can also find great software in the Synaptic Package manager (System -> Administration -> Synaptic Package manager or command line: sudo apt-get install what_you_want_to_install).
Unfortunately most of the time it's just knowing where the best software is.