TFS for tracking effort in a sprint. And I no longer take notes -- our sprint planner takes notes in individual user stories.
Todoist for task management outside of TFS (and also for personal tasks)
(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.
I have one section that contains a Note for each week. I archive the notes after awhile. Each week I start a new Note for that week, and update it daily. At the top, I keep my task list of things to do. When I go to copy it to the next week's note, I rank what's important and not.
I have a section called "projects" where I create a note for each Major project I'm working on. Here's where I create a Dashboard for what's going on with that project.
I have a section called "company" where I create notes related to my big companies process/procedures.
I have a section called "releases" where I have all the release notes stored of all the features that have gone into the project: this is so I can find almost anything instantly with the search functionality. I also have a note called Current Release, that I use as a scratch pad for the current things going on.
In general, any important email that I need to save from Corp, I transpose into my OneNote notebook. I also link a lot of my TODOs that I need to have deadlines on into Tasks in Outlook (I don't do this on my Mac.)
Anyway, I"ve used a lot of tools, like Org-mode, Evernote, Reophnotes, nValt, etc....and have been happy with the tool called One Note.
Etc....