http://docutils.sourceforge.net/ is quite nice: A rich set of features, easily extensible by custom directives, Python, and a hell lot of export formats (LaTeX/PDF, HTML, S5 slideshows, ...).
That's quite nice. Still not sure how I feel about wiki-style plain text markup formats though. I like them for simple and short docs, emails, and README's because it looks good in the editor, but it seems like the more you ask from that sort of format, the weirder things begin to look as you add features to support writing larger docs (and you end up with more syntax to memorize as well).