We use Sphinx as the main search indexing system on our clients' websites. It's a more powerful system than we even scratch the surface of, and allows us to index data from a variety of sources. Sphinx
We use Sphinx because it's the standard for Python documentation. As Paperless is Python-based, this only made sense.
Additionally, readthedocs.org plays very well with it, so that's your documentation hosting for you for free.
Finally, it supports ReStructuredText, which is amazingly powerful.