I ran across DocuWiki when viewing the documentation for Quicksilver. The output is very attractive and well organized. This looks like a great option for software project documentation. It appears as though it could handle most all documentation needs for small development shops. From the website:

DokuWiki is a simple to use Wiki aimed at a small companies documentation needs. It works on plain texts files and thus needs no database. It has a simple but powerful Syntax which makes sure the datafiles remain readable outside the Wiki.