How can I quickly and easily index my hand-written notes? 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?
Disclaimer: I do not endorse any of the products in this answer, nor have I necessarily used them in the past.

I've circumvented this problem largely by switching to Microsoft OneNote on a Lenovo Thinkpad Yoga with a stylus. For me, it gives me the best of both worlds: highly-accurate handwritten notes on a digital platform. (I only wish it was an open-source solution!)

That said, if you aren't interested in using a stylus/electronic means of taking notes, here's a couple of suggestions:


Check out a product like the Livescribe Echo pen. Using their special paper, you can take paper notes, get a digital copy stored on the pen, and record the audio of the lecture (synced with the notes themselves). There's also the Evernote Moleskin notebooks, which are specially-designed for OCR.
Before (or after) each diagram, provide a little description of the diagram itself. That way, if you use OCR, you can search for the description instead of the diagram/equation itself.
Learn LaTeX (for the equations, at least). It's not perfect, but once you've got a good idea of how to write an equation in LaTeX, you'd be surprised as to how quickly you can type them in.
As you pointed out -- after scanning the notes in, annotate them yourself using an electronic PDF tool. Most of them let you add comments that can then be saved (and searched).