I agree with what others have said, that there is no best system/framework because it depends on the use-case. But I haven't seen Sphinx (which I'm currently attempting to use) here, so I'll mention it. It's often used for web-based docs but has built-in PDF output via pandoc. The Hitchhiker's Guide to Python is one example of a book produced with it:

https://docs.python-guide.org/