I use LaTex for a lot of my note taking (for typesetting all equations certainly). When I first started using it, I remember the absolute horror of trying to get it to work with BibTex. The learning curve is relatively steep for non-programmers (I learnt it basically in parallel with learning to code) but it's certainly one of the most valuable tools I've learned and one I continually come back to for a huge range of…
* A directory and git repo for each paper (use your own VCS as desired)
* A separate git repo for my global bibtex file and a few heavily used .tex files (i.e. tcilatex.tex for sciword coauthors); this repo is set up as a submodule for all of the individual papers and they refer to their local version of the bibtex file.
* Really short, memorable bibkeys in the bibtex file (I first saw this recommended on I think stack overflow, but can't find a link right now). For a single author, first three characters of the name and last two characters of the year: Engle (1982) becomes Eng82; (by example...) Engle and Granger (1987) becomes EnG87; Sargent, Williams and Zha (2006) becomes SWZ06; etc.
This way I can just type most of the citations I need off the top of my head. The few I can't remember, I'll forget the year and searching by the first author via reftex takes about 5 seconds.
But, more and more for personal and not-for publication notes, I find myself just typing in the unicode and sticking with a plain text file.
edit: I'd love to hear other people's setup too, it took me a while to converge to this one and I'm sure there are better approaches.