Drupal standards are to use PHP doc blocks for API documentation. Drupal core API Documentation uses that - with the API module to display them in nicely human readable format. Contrib modules are unfortunately wildly variable in quality of documentation - but for a bunch that I work with/use/contribute to I've set them up to generate the documentation here.

Note: technically the [FR]/[EN] button works, but all the documentation is in English (as Drupal standard is) so even more useless here than elsewhere.

Here is the current list of projects I have documentation being generated for - if you have a specific one you want, contact me. Another note, re that variable quality? A lot of it is pretty bad. Quality documentation could be a great contribution to most any module.