Every few months history Twitter runs a thread about what software to use for note-taking. (See, e.g., threads recently started by Austin McCoy and J.Meléndez-Badillo.)
I wrote a whole chapter of The Princeton Guide to Historical Research on this topic, the gist of which is that historians have mostly abandoned our simple, easy-to-teach system based on 5 x 8 inch notecards, but we have yet to settle collectively on a computerized system to replace it.
Here are some more thoughts along those lines, and an explanation of the centrality of FileMaker Pro to my workflow for major projects.