I did similar research about two months ago, and in the end I went with node-webkit. The biggest upside on node-webkit is node.js and npm. The package management of npm is really nice, and node has well done filesystem access.
Brackets-shell looked interesting, but other than a nice IDE I didn’t really get what made this one as good or better than the rest. They are very clear that “The brackets-shell is only maintained for use by the Brackets project “, that screams run away to me.
Atom-shell seems to be recently active, but it seems much like brackets in that they are really writing and editor/IDE that just happens to be attached to a webkit runtime. It also is built on top of node.js. This one has the downside of being difficult to search for stuff online without being reminded of your middle school chemistry.
I really don’t want an new editor, and most programmers have their favorite already. For the actual application development, they pretty much work the same, and should, since they all use webkit. You basically write 90-95% of it like a website, and then deal with the native parts, and some config.
These things are true for all three of them
platforms – runs on Windows, Mac, and Linux
The big caveat on webkit is codec support. Typically you will have problems with non-free video codecs, unless you rebuild the dll/so to support them. For example the shipped node-webkit won’t play mp4 video.