Having tried a lot of tools including paper notebooks, mapping, personal wikis (ex. TiddlyWiki), tagged note-taking apps (ex. Evernote, Day One journal), blogging platforms, ... I've come to the conclusion that nothing does everything that I want as well as good old markdown.
My solution is a simple but flexible git repo [0]. So far I've logged notes on 50+ items over about a year, including books, courses, videos, magazines, podcasts, etc.
Some of the best examples are Show Your Work! [1] and Cities and Ambition [2].
P.S. One recent development is GitBook (https://www.gitbook.com/). It's a little more than I need personally, but incredibly cool software nonetheless.
[0]: https://github.com/tedmiston/notes
[1]: https://github.com/tedmiston/notes/blob/master/books/Show%20...
[2]: https://github.com/tedmiston/notes/blob/master/essays/Cities...