This is the best bible note-taking system that I've found. It pulls from the Zettelkasten system as well as Jonathan Edward's Miscellanies.

It takes some set up, but once you've got your system down, you've got a future-proof system.

__REFERENCES__
http://www.atom.io
http://www.biblenote.pro
http://www.evernote.com
http://www.notepad-plus-plus.org
http://www.notion.so
http://www.onenote.com
http://www.sublimetext.com
Jonathan Edward's Bible System: https://youtu.be/fqq-4-LiFVs
http://www.zettelkasten.de
Plain Text Bible https://1drv.ms/u/s!AiVS1iVtfil5iPgFaCEHS639udVirA?e=l7SYTd (This link looks sketchy, but it's what OneDrive gave me)
...
https://www.youtube.com/watch?v=8cdB1Any77k