How can I quickly and easily index my hand-written notes?
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).