I save my decks on a draft in Gmail. This means that I can access my list wherever there is an internet connection. I organize everything on my draft.
I have 3 large headers: Mono, Duo, and Rainbow.
The Mono header is subdivided into each of the 12 elements.
The Duo header is subdivided by "Class": Flying Weapon, Unstable Gas, Golem, and Fractal are examples of these "classes".
The Rainbow header just has a bunch of rainbow decks in it.
Unupgraded decks are put below their upgraded counterparts.
It's a rudimentary system, but it works.