[Programmatic]

+1 to OneNote. The Notebook/Section/Page paradigm is super intuitive and convenient. You can create/copy hyperlinks to different notebooks/sections/pages/paragraphs, so it's easy to make a master notebook with shortcuts for navigation.

(un)fortunately I'm standardized on OneNote 2007, vs. the later versions, but keyboard shortcuts for it in 2007 on Win7 are fantastic. Win+Shift+N to bring up OneNote with the last page open, Win+N for a new unfiled note, and various "tags" and searches. Many Win key shortcuts have changed in Win 10 and later versions of OneNote.

I use checkbox tags for Ctrl-1 (you can assign Ctrl-# to particular tags), so you can easily make a checklist by just typing an item and then hitting Ctrl-1 to make a "todo". You can mark it as done by hitting Ctrl-1 again on the same line. You can also insert timestamps with Alt-Shift-F so you can note when you completed something or similar. Win+S brings up a screen snipping tool for quick documentation on a topic as you go.