For what it's worth, my experience (1 yr) with Trac has been favorable. It's nice because it couples tightly with the source repository. We use it to track progress towards milestones, relate changesets to bug reports/fixes and for some documentation/reference. Supposedly it plays with doxygen, (http://www.trac-hacks.org/wiki/DoxygenPlugin) but we haven't tried that yet.
I have not used MediaWiki.

-Nate



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