Well.. for analog .. er.. non-digital notes, they are mostly scribbles of some problem I want to solve..which are all related, because I tend to solve problems that are directly related to my research. I keep two notebooks. I solve a problem in a notebook, and then when I see that my solution got messy.. I move to the other notebook and continue solving maybe browsing at my old solution in the old notebook. So I use one or the other notebook alternatively for trying a problem.. I usually finish the problem in one notebook, but if it gets really complicated the continuation goes on the second notebook.. and I don't try to categorize the problem... I just continue until the notebooks are exhausted then they are archived and I use another set of two new notebooks. Those are my problem and brainstorming notes..
For notes from seminars or whatever else.. I have just one notebook for them all (you dont tend to organize the notes once you reach graduate school and you hardly go to classes). And I usually find what i want in them.. because I dont tend to make notes on seminars talks that I don't understand at all or that I think will not be able help me in the future. And I often take note of keywords rather than the whole seminar talks.
For digital "notes".. they are organized by subject: Algebra, algebraic geoemetry, number theory, topology, ..etc. I often even have folders by names of authors (who are very well known in the field and whose works I often browse) within the say algebra (or whatever) folder. Those are for papers. For mathematical ebooks, I have my own folder I called Mathbooks and I should get organizing them by subtopics as well. I practically live only by digital media.. my 2 notebooks are the only nondigital things I currently depend on in doing research.