[acidburnNSA]

As much as people don't really like it, reStructuredText with Sphinx is still my favorite one of these. Once you get into wanting to do fancy things, the sheer power and extensibility of it with custom directives and community plugins is hard to beat. The glossary, index, and project cross-referencing features (intersphinx) are amazing. You can easily integrate with Bibtex reference libraries (maybe managed in Zotero). You can do full-on traceable QA in it, not just for software, but for hardware projects as well using e.g. sphinx-needs [1]. I think for some sophisticated applications, reST + sphinx is best.

And of course you can write some pages in this ecosystem in Markdown if you want using MyST [2]

[1] https://sphinx-needs.readthedocs.io/en/latest/

[2] https://myst-parser.readthedocs.io/en/latest/intro.html

[boxed]

I've used it for a few years but still have to look up how to do references and links every time. The API has some hilariously bad parts too (you must mark a section link above the heading, but in the AST it's then not part of the section.. why!?). It's also quite slow, and has silent failures that produce garbage in the output sometimes.

[danmur]

It's a bit more effort but it just can't be beat for documentation.