Box 1: Lands and Artifacts, sorted alphabetically.
Box 2: Black cards, " ".
Box 3: Blue cards, " ".
Box 4: Green cards, " ".
Box 5: Red cards, " ".
Box 6: White and Gold cards " ".
I also have binders of complete sets from The Dark thru Urza's Destiny. When a set rotates out of type II, I put that set in a binder. I'm still working on Legends, Antiquities, Arabian nights and Unlimited.
I have tradable rares in a seperate binder, uncommons in a seperate box, and commons in two 3200 count boxes, which are nearly overflowing. These cards are sorted by color, but not alphabetized.
And one more thing: my collection of 1,000+ (I quit counting) Pestilences are in a seperate box.
It was lots of work to organize originally, but I can put my hands on any of my 30,000+ (I estimate) cards in seconds, provided I can remember the name of the card!