This might sound nuts, but I have settled on a three step process that mostly involves keeping most notes in my head.
Step 1 is using the method of loci (MoL) to memorize up to 30 things throughout the day. For context, MoL is a strategy where you visualize things you want to remember in a room. I have one "room" for each day of the month, with 10 spots in a room, and will often visualize up to 3 things in a spot (so 10 x 3 = 30 a day). I have 4 paths that each lead between 7 rooms, one path per week.
Step 2 is just keeping a page of notes per day in a planner. This is really helpful for jotting miscellaneous things down (like future things to read, possible connections).
Step 3 is that often as I'm thinking back over notes from step 1, or reading new things, I'll want to sort of "put it all together", or write up something that cuts across multiple days. There, I'll often refer to my planner, and might start a spreadsheet to keep references on.
I think the problem before was that I'd wanted to write useful longterm notes when first learning / studying something. But that's probably when I'm least qualified to take really insightful notes. It's been nice to let things marinade, and focus on keeping the "building blocks" around!
https://en.wikipedia.org/wiki/Method_of_loci