One of the things I really need in my notetaking is some organization. I tend to write a lot of notes and then lose track of them within a short time. This may be okay in general - notetaking is a process to organize one self and does not need to provide some organization from the get-go. Nonetheless I would really like some organizational tools like links to other notes or some scoring for tags to assist there.
One thing I started doing to organize in with the tools already available is adding tags of the form year.month.day to notes in order. Together with the folder extension this builds a timeline which I can reference back to. Although I already dread the huge folders for full months later in the year. Maybe I will have some idea down the road.