I use a lot of HTML for documentation.

On one hand, I can produce XHTML that may be imported into Word and then further into nice page-breaked pdf files.

On the other hand, I may use php to auto-generate the HTML, allowing me to store information in either a flat text file or a MySQL database.

I also try to incorporate tags into the source code to allow specific conditions in the code to be mapped to specific requirements.

Anyone used Doxygen together with graphing of relations? Unix have a nice set of tools that can read text files and auto-create graphs showing relations between states or objects. And even if you don't have 100% control of the layout, it is very easy to produce the text files and have the tool compute a suitable layout.

One of the advantages with php is that it not only can be used to produce documentation - it can also be used as a prototyping language to test different things - and the large availability of library functions/classes means that the output from simulations can be easily presented in a suitable form, while at the same time input parameters can be harvested/retrieved from other systems or from files or images...