The best way to do this would be to use the experimental pandoc support for Andrea
Rossato's hs-citeproc.  This would allow citations to be written in a markdownish
format and exported not just to HTML but to all of pandoc's output formats. 
hs-citeproc also has bindings to bibutils, which allows it to read bibliographies in
many different formats. For details, see http://code.haskell.org/citeproc-hs/.

So, John, what would adding support for hs-citeproc mean from the standpoint of
gitit? I presume you'd need to make a few tweaks to enable this?

The main bit of work is figuring out how to specify a bibliography file.  If the file
is xml or bibtex, it could just live in the repository as an uploaded file (though
this would make it visible in the wiki - perhaps that's not always desirable). But
there would still need to be some convention for specifying which bibliography to use
for a given page.  Ideas welcome.

I guess the best balance of ease of implementation and use and generality is to have
a single global bibliography file, which could optionally be marked private? I could
imagine some useful UI stuff could later be built on top of that using Javascript.

BTW, might be nice if Andrea can at some point add optional RDFa support, so that the
HTML content can be tagged for easy extraction.