To the right of my workspace I keep all of my embellishments. They are in plastic compartmentalized boxes ($1.95 ea. from Wal-mart) by color. It is amazing how much stuff these things can hold once you start taking emellishments out of their packaging! Just above the embellishments is a little shelf that has a tray where I like to toss my scraps. There is also a platic box that holds all of my Palette Ink pads.
Use Tic Tacs containers to store brads, eyelets, beads, any small items. Makes items visible, keeps them sealed, and allows for dispensing the items. Storing the containers is easier and more space efficient than the round varieties.