For my use cases, I care about writing software documentation, and also rendering Python API documentation - the special "docstring" documentation comments within Python source code. See PEP 257 - Docstring conventions for Python style guidelines. I currently use epydoc for this, which supports a range of markup languages including its own epytext markup language. Another potential choice is Sphinx, which currently only supports the reStructuredText markup language.
For larger documents including my PhD Thesis and scientific papers, I like to use LaTeX. This is really powerful for mathematical markup, but also makes cross-references between Figures, Tables, and document sections pretty easy. It is far more popular in Mathematics and Physics than it is in Biology.
And for online repository and wiki hosting BitBucket supports several markup languages, while GitHub supports even more markup languages,
MarkDown would be a nice choice, but even if we ignore Sphinx, it looks like for a Python project, the only sensible choice in terms of broad tool support is currently reStructuredText.