Personally I like Robodoc quite a lot. One can use the same format to document a lot of programming languages (Perl, C/C++, Java obviously) and generate documentation in various formats (HTML, LaTeX, RTF, etc.).

It runs on windows, unix and probably almost every operating system with a C compiler and a shell.

You can find Robodocs home page here. I've used version 3.x quite a lot and was happy with it. The latest version (4.x) should have an even richer feature set.

Just my 2 cents, -gjb-