Joplin[1] seems to be the best in my view. It's cross-platform, has decent sync capabilities, plus a web clipper. I've been using this for a while and have liked it a lot so far.
I used Quiver[2] for a while when I used to run macOS, but moved away from it because it was macOS specific. It also had some features lacking, namely no spell check (an issue that Joplin also has, although I believe this is being worked on). It also dosen't have a web clipper.
OneNote is ok, but I don't run Windows (I used it at work at one point). The killer feature it has is collaboration with other uses on the same domain, a la Google Docs. If that's not a use case you have, it's probably not worthwhile. Also no web clipper.
I briefly tried zim[3], but found that it lacked polish, and didn't have a mobile client or a web clipper, so I never fully moved on to it.
For a long time, I used Sphinx[4] plus several extensions and wrote everything in rst, with syncing accomplished via git. This turned out not to be very ergonomic to use, had no mobile client, and no web clipper.
Some other note taking apps that I've heard of but not tried personally:
* Turtl[5]
* TagSpaces[6] - tried the demo briefly, but didn't like the UI, also the iOS client was abandoned at that time
* Standard Notes[7]
* Inkdrop[8]
1 - https://github.com/laurent22/joplin
2 - http://happenapps.com/#quiver
4 - http://www.sphinx-doc.org/en/master/usage/restructuredtext/b...
6 - https://www.tagspaces.org/