hmmmmmmm here is a Take
bring back wikis
seriously. set up a wiki for your next reverse-engineering project. no matter what the note-taking app du jour is, a wiki's going to be more flexible and useful. make a bunch of pages! make a page for a memory map! make a page for the loader logic! make a page that's just tables of file format headers! link them all together!
a thing that didn't catch on but should've: interwiki links! you can do something like [[wp>Executable and Linkable Format]] in your wiki's markup and it'll produce a link to the Wikipedia page on ELF
@er1n i been using vimwiki for about a year now for my personal working notes.
it has weaknesses, but i think maybe single-user or very-small-community wikis are actually the sweet spot for the form.
(i've also spent way too much of my career trying to get groups of people who Don't Get Wiki And Never Ever Will to use wikis, and it has generally been a litany of suffering, and i'm never doing it again if i have a choice in the matter.)