I've been enjoying the Bullet Journal system for utilizing a paper notebook. The idea of using one whole “spread” of two pages for a specific topic is particularly appealing. I also like the index idea.
All the items I want to record in a notebook are of the notes variety. The other main entities of the bullet system (events and tasks) are well-covered by my digital tools (namely, iCloud calender and Omnifocus).
The Bullet Journal system keeps my paper notes organized and accessible.