OSX applications preferable, but feel free to recommend apps for other OSs for fellow HN readers :)
Personally, I like GitHub flavored markdown and a text editor. There are programs in all of the popular languages to convert that to HTML.
We tried MS Word years ago. The zipped 2007+ format makes the git repository blow up, so we dropped it.
Sphinx Doc: http://www.sphinx-doc.org/en/stable/. Builds on top of Docutils. Allows API documentation (http://www.sphinx-doc.org/en/stable/ext/autodoc.html) and cross-documentation linking via intersphinx (http://www.sphinx-doc.org/en/stable/ext/intersphinx.html). epub, PDF, and html output.
I've created mini technical manuals at previous workplaces using sphinx.
More clickables:
For graphs, grab aafig: https://pythonhosted.org/sphinxcontrib-aafig/ or graphviz http://www.sphinx-doc.org/en/stable/ext/graphviz.html
For enhanced python documentation (numpy and google style api docs) http://www.sphinx-doc.org/en/stable/ext/napoleon.html
For creating your own API docs outside of python use sphinx "domains" (http://www.sphinx-doc.org/en/stable/domains.html):
- HTTP: https://github.com/deceze/Sphinx-HTTP-domain
- .NET: https://github.com/rtfd/sphinxcontrib-dotnetdomain
- JS: http://www.sphinx-doc.org/en/stable/domains.html#the-javascr...
- C++: http://www.sphinx-doc.org/en/stable/domains.html#id2
- C: http://www.sphinx-doc.org/en/stable/domains.html#the-c-domai...
- Scala: https://pythonhosted.org/sphinxcontrib-scaladomain/
- golang: https://pypi.python.org/pypi/sphinxcontrib-golangdomain