Isn't it obvious? Use the one for your language. If you write in Java, JavaDoc, for C or C++ there's Doxygen, Erlang has its EDoc, Perl commonly uses POD, Pytho

Isn't it obvious? Use the one for your language. If you write in Java, JavaDoc, for C or C++ there's Doxygen, Erlang has its EDoc, Perl commonly uses POD, Python usually is documented with its native docstrings extracted by Sphinx. This way your API and documentation sources for it resides in the same place. Also, much depends on what you expect from the tool, as there are approaches that decouple documentation from code.