Currently, I'm using Sterilte organizing trays from Target. They have three trays each: Bottom is for the largest tiles and longest. Middle for the medium length and mid-sized squares. Top for the single and smallest tiles.
It works fair enough, but I'm thinking I will upgrade to baggies, with each exact type in specific bags (all 1 square in one bag, etc...) to make it easier when putting a room together on the fly.
Ktulu