For many decades I've done this with my work notes. I use a cross-indexing scheme, using square brackets to mean "this uses information in item X" and angle br

For many decades I've done this with my work notes. I use a cross-indexing scheme, using square brackets to mean "this uses information in item X" and angle brackets for "this is used by item Y". The latter is really important, because if I find an error in an early note, I can trace it's effect easily through later work. My reference scheme is simple: X and Y are of the form B.P, where B is book number and P is page number in that book. I write these X and Y items in the margin, where they are easily visible, and later I copy them to the first page of the entry. In addition to the above, I use keywords, and these go in the table of contents along with titles. Every once in a while, I transcribe the table of contents and the cross-indexing information into a computer file, so that I can do logical operations on the data and find things I need. None of this takes much effort, and it comes in handy when you're doing quite a lot of work at once.