New Redemption Grab Bag now includes an assortment of 500 cards from five (5) different expansion sets. Available at Cactus website.
First I sort them all into types. Then I take each type, and if applicable, sort them into brigades. My brigades are sorted alphabetically (Blue, Dual, Gold, Green, Multi, Purple, Red, Silver, Teal, Tri, White; Black, Brown, Crimson, Dual, Gold, Gray, Multi, Orange, Pale Green, Quad--coming soon!). I then take each brigade and sort them into sets, and alphabetize those (Angel Wars, Apostles, C/D, Disciples, E/F, Faith of Our Fathers (2007), Faith of Our Fathers (2011), G/H, I/J--coming soon!, Kings, Patriarchs, Priests, Promos, Prophets, Rock of Ages (2008), Rock of Ages (2011), Rock of Ages (2013)--coming soon!, Thesaurus ex Preteritus, Un/Limited, Warriors, Women. Finally, I take each set, and alphabetize the card names.Once that is done, I take out any cards that I have more than 4 of, and put those in my extras box/folder. I then take out any cards that I can never see myself using in a deck, and set them aside in separate card boxes. Then the boxes I take to tournaments/build decks with have just the cards that I would use. Every once in awhile a card makes it from the minor leagues to the big leagues if I find a use in a deck for it. For example, Isaac and Joseph from Patriarchs were recently upgraded for my latest iteration of my Zebulun deck, so I could use Lifting the Curse, Benedictus, and Consider the Lilies; and Goat with Horn (Prophets) was upgraded so I could get Name-on-Name bonus with The Goat with Horn (and in my most recent tournament, I successfully took down a Simeon+AutO-->Moses band using him). This works well for me, but it requires dedication and a bit OCD. But it helps me be able to put together a T2 deck from a list in ~10 minutes or so.
Your system intrigues me, but the one hang up in it for me would be I don't want to keep extra's of reprints. For example you say you keep 4 of a card and put the rest in extras. Lets use Battle Prayer for example, If I have 3 Warriors BP, and 2 Kings I would prefer to have a system that would allow me to only keep the more useful one so for me I would keep the 3 warriors ones, and only one of the Kings version. I had considered a system like yours in the past, maybe I can find a way to merge them, I like the set sorting because finding the newer cards would be much simpler.
I actually sort of address that hangup with my last point: separating my collection into "deckable" and "non-deckable". Battle Prayer is a bad example from my persepective, because there is value to each version (the Warriors one is better if you use evil gold enhancements, and the Kings one is better if you prefer the additional 1 point of strength for Moses, and don't use gold evil enhancements). In cases where they are exact reprints (or no advantage to one version, like Great Faith Women's vs. H-deck) then I put the less useful one in my non-deckables. That way I don't have to sort through them. Of course, my system assumes that I own 4 of every card (regardless of version), so it probably doesn't apply to most people. The set sorting is very nice both from a deckbuilding standpoint, as well as from a knowledge-of-the-game standpoint. The first set that I collected was Warriors, and during that time I was able to more or less memorize how many Characters and Enhancements come from each brigade in the Warrior's set. It also makes it easier to separate the "deckables" from the "non-deckables" (since there will be more "non-deckables" in Un/Limited, Prophets, C/D, E/F, etc., than the newer sets).
My cards are organized by Bible verse. It's awesome how many Redemption cards have been made, how vast and diverse the cards are as far as their Bible content, because when you put them all together by verse, it's like reading through the (fully-illustrated) Bible!