What is an efficient way to organize my magic collection?
There are a lot of ways to organize your cards that are efficient. What it is going to come down to, is what sort of efficiency are you looking for.

Deck building efficiency - This is pretty much a non-issue if you use digital deck builders, but if you don't know exactly what cards you own, it is helpful in finding possible alternatives for cards you want to run but don't own. Because all cards are near other cards of the same color/type, it is easier to find cards to fill out your deck.


Color, Card Type, Mana Cost, Alphabetical


Card finding efficiency - This reduces the size of all your box divisions, making it easier to find a particular card. 


Set, Alphabetical (or collector number)


Trade/Deck Idea efficiency - Separating the Rarest cards from the most common cards allows you to easily find more valuable cards, or cards that an entire deck can be built around.


Rarest/Non-rare, any other sorting criteria.


Size efficiency- With many of the other sorting types, you may try to separate the individual Colors/Sets by placing them in their own box and filling up empty space with deckboxes or basic lands. When you organize for space, you need to only separate sections with index cards cut to fit card sleeves.