Somewhere around November last year Jure introduced me to Bullet journal. Despite its chilling name, it's simply a set of recommendations on how to organize day-to-day notes and to-do lists in a plain old notebook. I gave it a try and experimented a bit with the way I put things down on paper. Here are some thoughts on the topic after a few months.
I've always kept a notebook with me. Before I started using the Bullet journal, I usually went through one 80 page notebook per year. Now I use up around 20 pages per month.
I don't think I write that much more than before though. I now leave much more space around notes for later additions and I typically start a new topic on a new page. This means that notes are less crowded and more readable after a while, but also sometimes a page will remain three-quarters empty if I don't return to some particular thought.
Previously I did a lot of random notes on various scraps of paper and printouts which invariably accumulated on my desk until they got lost or thrown away. I now tend to do all notes directly into the notebook. Sometimes with pencil if I predict a lot of corrections, but usually with ink. Annotated printouts get taped between the pages of the notebook so they don't get lost.
Every once in a while I tend to do a brain-dump page with lots of assorted tasks that sometimes pile up. But normally I keep notes and tasks organized under a common heading that spans one, two or three pages.
The biggest improvement that came from Bullet journal are the indexes. I number the pages and I write out an index page once per month. I group individual topics in the index by projects. I still keep dates in the margin of pages. I don't keep per-project indexes, but I plan to make a yearly index of projects. Page numbers don't restart when starting a new physical notebook.
I think indexes are really what made the notebook read-write and not only write-only. It used to be that in my old notebooks I only kept going back to a few pages with the most important notes or recipes that I had to keep looking up. Now I find myself daily browsing back to read a thought I have written down a month ago.
Using square boxes for marking to-do items is also a very good idea. I used to mark to-do items with arrows, but boxes are much more visually distinct and allow for quickly scanning the page for un-checked items. I don't use all of the marks described in the Bullet journal tutorial: I either check the box to mark it done, cross over the line to mark it not relevant or draw an arrow over the box to mark that the item has been moved to another page. This last one is fairly rare, since it's easy to look up past unfinished tasks.
Contrary to the Bullet journal proper, most of my notes are not organized by bullets. They tend to be a mix of sketches, bits of text, diagrams, and calculations. Often my notes start in the paper notebook and continue into a IPython Notebook or some other digital file.
For now I usually write down which digital file is connected to the paper notes and vice versa, add a comment in the file pointing to a paper page number. I try to keep duplication to a minimum, but between the notebook, digital files and project documentation which has to be shared or filed separately, there is necessarily some overlap.