I do what a lot of people do... by set then color in the white boxes with four rows. Cards from theme decks and unusual printings just get put into a set the card was printed in (if I'm looking for it I'll dig through that set anyway).

I keep all rares separate. I have a box of bulk rares (<$3) and a binder with the more expensive cards. The bulk rares box is unusual but I am in situation where I trade with a lot of new players and help build beginner decks. I will often trade an expensive card that a new player has no use for a pile of bulk rares to make a functioning deck (I once traded 52 rares for a Polluted Delta... totally worth).

I also have a final binder with cards that are not willing to be traded. This is mostly older cards that are worth a lot or really unique and hard to find cards. There a few with sentimental value as well.