Research indicates that taking notes by hand is better than using a computer, for long-term comprehension (source). As an engineering grad student, I also find that using pencil and paper for graphs, diagrams, and tables is much quicker and easier than keyboard/mouse (or even stylus).
To circumvent the issue of losing my notes, I take them on loose sheets of letter paper, then drop the stack in a feed scanner every week or so, and the file to a backed up folder on my laptop.
But here is my issue: later on, when looking for specific items in my notes, it is hard to find things without scrolling through the whole PDF. Even if OCR was reliable with handwriting, it would be little use or circuits, diagrams, complex equations, etc.
So, is there a quick and easy way to index these notes, perhaps adding something like bookmarks or an index?