- Org Mode (with org-superstar) for taking notes. Everything gets saved into a Microsoft OneDrive for sync between my laptop and desktop machine.
- Org tasks and org-agenda for project planning. Far less disruptive to your train of thought than busting out Microsoft Planner to remind yourself to follow-up on some line of research or whatever.
- pdf-tools for viewing PDFs. It's a bit kludgy (it renders PDF pages to PNGs on the fly because that's what Emacs can display), but it's somehow still less CPU-intensive than Acrobat DC or anything based on PDF.js. PDF-tools has fast incremental search, and a fast occurs mode for finding and highlighting all hits in the file.
- pdfgrep and pdfgrep-mode for searching across PDFs. Hits show up in a grep-mode buffer and you can click to jump to the exact hit. (It uses libpoppler under the hood to confine the search to the PDF text layer and show hits in logical page order rather than PDF file order, which can be arbitrary.)
- org-pdftools for creating links to specific pages of specific PDFs in Org Notes (e.g. noting that the testimony for a particular witness starts on page 758 of some 2,000-page trial transcript).
- Built-in Emacs features (windows, frames, buffers) make it easy to juggle between documents and compare them side-by-side. Emacs Bookmarks make it easy to save your place and jump back to where you left off. It's shocking how many notes tools get this wrong and only let you see one document or attachment at a time.
I'm kicking myself for not having discovered this earlier!