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Brigade makes sense if you're making decks, like Joey said. Go to http://www.threelionsgaming.com/store_singles.htm and you'll find the sets in the order they were released.
What I was doing is taking one copy of each card and putting them into binders while the other ones were sorted by brigades in my big box.I also keep all my UR/FOOF up in a seperate tin and that's where my main trading cards are.
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I do not organize my cards at all, and I definitely do not organize them first by card type, then by brigade, then alphabetically, then by order of release. Also I do not keep the cards individually sleeved, or keep those sleeved cards stored in baseball card pages in three-ring binders, and certainly not with separate binders for "first set" copies and "second set" copies.