I'm using LiveComment structured notes for everything. I developed a methodology how to use it across multiple operation systems & technologies. LiveComment extend my memory & speedup developing source code. It has powerful server/client plugins system for add any function in runtime with live reload. I'm using paper & board for brainstorm too.

https://www.npmjs.com/package/livecomment

Samples here:

http://acpul.org/livecomment-src - livecomment js sources (it's quine, that developed using self documented code)

http://acpul.org/pool - common memory pool: active info, some processed bookmarks from HN, reddit, etc.

http://acpul.org/pica - livecomment in real project. here is collected info when i was develop gpu optimizations for popular nodejs image resizing library https://www.npmjs.com/package/pica