I just dump them all in a very appropriate, large storage bin - the hood for the 600 II.
Seriously, I store them on their lens (reversed), except the 16-35L II and TS-E 24L II, which I store along side the lens in the Storm im2720 hard case.
The nomenclature for hoods is EW for wide angle lens (use the wide end of a zoom), ES for a standard lens, or ET for a telephoto lens, the number is the diameter of the hood at the mount, a letter after the number is a different design for the same W/S/T + diameter (i.e. fits a different lens), and a II, III, etc. are revisions of the same design.