I use Zim Wiki ( http://zim-wiki.org ). My requirements, which it fulfills perfectly, are: open source, non-proprietary format, text file storage (which I store inside Dropbox, so that solves syncing), cross-platform, hierarchical notes, some sort of markup for section headers, highlighting etc., links to other notes. Zim Wiki has many more features, but that's enough for me.
Drawbacks: its search functionality seems to miss stuff sometimes, though I haven't figured out why yet. So I'm used to using ag (silver searcher) when I can't immediately find something.
Drawbacks: its search functionality seems to miss stuff sometimes, though I haven't figured out why yet. So I'm used to using ag (silver searcher) when I can't immediately find something.
Edit: added cross-platform requirement