Some use other systems - take a look at Python's Sphinx for example, they have a all-in-one doc system that build everything (it also works for C/C++)
I always think of documentation as being separate to the code, doxygen is great, but it is for an overview of the API, not 'documentation'. For that, a wiki is great, but I prefer to use ASCIIDOC and store the results of that in source control along with the code, mainly because I can generate PDFs from it to hand to other people (eg the testers, customer, etc)
