Pencil and Paper FTW. I'm still trying to get used to my wacom tablet. (wishing I had paid for the bigger one).
The nice thing about pen and paper is that you can go back through all your brainstorms and trial designs for that project or even hash through the old ones to see if something that didn't fit one project might fit a new one. On a pc most people if like me, delete and are done with it.
Programs I use:
Flash, Illustrator, Photoshop, After Effects, Premiere, Final Cut, 3D Studio, Director, Notepad, Dreamweaver