For brainstorming and architecting I use whiteboards that I take photos of before erasing. If there's no whiteboard available, I use pen and paper - yellow legal pads - which I also take photos of.

Text files and Evernote I use for snipping web pages, organizing bookmarks, and taking meeting minutes. For todo lists, I use text files, Evernote, and increasingly, Asana.

I don't do any brainstorming with the computer.