Over my last two terms I've invested in using markdown with Pandoc to write any notes in class. I needed a way to be able to take math notes, and be simple to use. After migrating to Linux, OneNote was no longer an option. It's simple to use, as it uses markdown syntax for anything text based, and LaTeX syntax for inlined math formulas.

I as of recently also found out that VimWiki exists. I've started to use it because of the note linking capabilities. I'm starting to keep notes on events, certain tools, languages, and all other information I need in the wiki. It's also in Markdown which is nice.

Find tools that are close to what you want, and try to make your own suite. It may seem like a lot of work, but knowing your note taking solution inside and out can be very handy. When you're presented with something new that you don't know how to take down, you can evolve the system into being capable of handling it. Which you can do if you've make your own system, but using ready made solutions won't allow this.