[imurray]

Part of me wants to just hand-write them and then maybe scan them, but that's not searchable/indexable, and doesn't lend itself well to version control.

I'll comment as someone who does hand-write and scan my notes. I date and number every page, then put a pile through a sheet-feeding scanner every so often. Sometimes I put date and page numbers in my code comments, so I can find my notes on where the code came from. I also enter a line of text (or more if necessary) about each scanned page so I can search that. Something I do in a brain-dead moment every month or two. It can be interesting to look back through the notes and see if I've forgotten about anything interesting.

Often I'll write out the math for something multiple times before I really understand it, and using a pen works much better for me. Only a small fraction of what I write out is worth TeXing up.