If I'm learning I will write notes with a pencil and paper (pencil over pen every time). This means I have to think more about what I'm writing and for me is more flexible. I use an A4 squared pad with an index at the front, each page is split similar to the Cornell note taking system which is good for summarising and adding tags for quickly finding information. My notes are scribbled and messy. I will then transcribe these onto a computer using text files and folders for structure. You can't beat text files. As a front end for this I use Zim Desktop Wiki. Cross platform, portable, and easy to use with a simple markup syntax. It offers many excellent features, including a journal, tasks, diagrams, spell checking, interlinking, back links, searching, tags, images, tables, version control, and many others. Drop the notes into Dropbox and you have syncing.
If the worse comes and Zim disappears it's all just text files and folders. Pandoc can convert Zim to markdown or whatever you like.
For other quick notes I use a reporters jotter. I will transcribe them onto the computer if they are important. But generally these notes are throw away.