I use Dokuwiki for documenting an open source project I'm working on, and I have found it to be very good.
However, there are a few things I miss, and one of these things would be easy to implement on your side.
I would like to mark up my documentation with "smileys" (not the happy faces in this case, but FIXME and DELETEME). Some I would like to add are NOTE, WARNING, and probably some more also. I could add them myself to conf/smileys.conf, but then those changes would get lost when I upgrade (and conf/smileys.conf would get replaced)
So a smileys.conf.local file or similar would help me, which wouldn't get replaced by any files in the new tarball. The same goes for the rest of the configuration files (mime.conf, entities.conf and acronyms.conf for example).