I enjoy this sort of post from other people, and it's been a while since I've done my own.
I pretty much live in Evernote these days. I like it because it syncs, and I can get to all of my notes when I'm offline as long as the device I'm using is updated. That's a pretty big distinction to me between it and Google Drive. (I haven't tried One Note, Maybe someday I'll look into it.)
I only use 4 notebooks. I have an Inbox where I put stuff that needs to be filed away, a Filed for things that just need to be kept, one for Lesson Plans where I keep all of my daily lesson plans, and one called Irons in the Fire where I keep my To Do lists.
I have a much more extensive set of Tags that I use for all of these notes. I like using tags more than notebooks as I can mark things with multiple tags, and I can nest tags.
Each project that I'm actively working on gets a note in Irons in the Fire. In that note I keep a running to do list of all the things that project needs me to do. Projects that I'm not actively working on get renamed to have "zzz" in front of the name so they go to the bottom of the list. Keeping these lists really helps with my personal stress level.
In lesson plans, I start a new note each morning for each of my courses. (courses that have multiple section only get one.) I use text expander inside these notes to dump in my blank lesson plan template. (If you have a Mac, and you don't use text expander, you are missing out.)
After a semester, I move those lesson plans over to filed. They are still tagged with the correct course, so I can find them again quickly. I should start cross tagging them with the Objective that is being covered. I realize after looking over my lesson plan template, it might be worthwhile to break that down in another blog post.
I've started using notebooks for general note taking (Either an old beat up Moleskine, or a Field Notes). I then use the scannable app to capture those notes and get them into Evernote so that I don't have to worry about losing them. As much as I desire to completely live in a digital world, sometimes nothing beats the old school way of doing things.