FWIW, I like using Markdown for manuals because it can be rendered out as HTML and PDF + it's easy to read plainly. So, you end up separating the content from the display which is great as it will make migrating in the future easier.
IMO, the wikis aren't nearly as nice as they're pretty slow, and rarely render acceptable PDF output. Plus, there's always too much added functionality and content on how to use the wiki, and all other sorts of confusing information. Lastly, IMO, their design is just not so nice.
Here's an interesting little Jscript WIKI called MDWIKI which if you put on your server (or I put on my dropbox folder) can automatically convert an existing .md (markdown) file AS IT'S RUN, so you don't have to always do the .md -> HTML conversion each time you edit your .md file.
