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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