Each lego set is in a Container Store shoe box with a label either cut from the original box or printed out from the internet (if we threw the box away too soon). Lost & found bits are in a box of their own. All instruction books are kept in plastic sheet protectors and sorted (by theme then number) in 3-ring binders!
What a fabulous post! We have around 50 pounds of Legos, it is overwhelming. Now if I could get my kid to keep the legos organized in the various systems I've started for him, I'd be in great shape. lol