For cementing understanding, I like carefully crafted notes on pen and paper, sometimes a first and second draft.
Otherwise plain text files. I organize my files by putting them at first randomly into one folder, and then sorting them as I refine them and make second drafts. This is nice because I can always sort by most recent - anything not very important or timeless goes somewhere else.
'Note taking tools' sounds like such a misnomer, a notepad is just to write scratch down in so you can focus on something more important. To elevate scratch to such a level of sophistication is missing the point - to really test your knowledge, you must be able to write about it and read and edit as the role of harshest critic. A good single text file or essay is enough to encompass very large blocks of knowledge - the rest comes from organizing those essays.
If you are studying for a test - then feel free to search for enhancements to memory, but to build understanding most of that organizational work will be taking place in your head, not a tool. When it is organized in your head it is easy to organize into a file, paper, or set of folders.