I see you didn't mention Markdown. My solution for the last couple of years to this problem is to have all my notes organized into folder and .md files. A couple of advantages: - I can move around different IDEs/apps since there are a lot of different solutions for every platform there. - Same goes for search and links between folders. Rely on git for version control of the files themselves. - It gives you the flexibility of using plugins to turn into PDF or host as a gitbook private site for example.

Knowledge base organization gets discussed frequently on HN. I understand your frustration though, I've always longed to see a one fit for all platforms though. Onenote sure shows a lot of potential but is probably limited by the fact that MS wants to keep it as close to their office suite as possible.