We use doxygen + markdown for high-level documentation. This way you can edit the documentation in a text editor and put the markdown files in version control.

We use doxygen + markdown for high-level documentation. This way you can edit the documentation in a text editor and put the markdown files in version control. And with graphviz and mscgen you can even create some standard graphs. The doxygen-generated html documentation is then put inside a wiki automatically.