When developing new projects I often found my self in the very same situation: I have read through tons of pages of manuals, wikis and books, and would like to create my own notes on the subject. Be it for a college subject, a new electronics project, or a complex subject I'm enjoying.
In any case, I need a way to add notes, attach files (e.g. PDFs, videos, source code, etc.) and insert images. Also, it's of upmost importance to be able to create hierarchical dependencies between my notes (i.e. subsections or similar) and be able to navigate through the data in an intuitive way that does not require tons of mouse-scrolling. And most importantly, the data must be easy to export and available offline, as I don't want to get stuck with any commercial services.
If you are in a similar situation, then read on.