How in Hades Do You Keep Track of Your Notes?

Okay, internets, help me out here.

I write. A lot. I have several universes in motion. I simply cannot focus on just one–it's not how my brain goes.

I tried a note box. It's worked some, but not as much as I need.

I own a file cabinet. I try to keep things filed.

I own tons of notebooks. I try to keep them separate. But then I'll have three pages of Dream'verse notes and in the middle of a paragraph will be a quick aside about an event in Flame'verse.

I have a lot of freaking notes.

Is there a way ...