You can organize them by: Type, Rarity, Illustrator, HP, Retreat cost,
Maximum damage, etc. Maybe you could also combine the attributse above.
I use binders to store all my cards (I'm a collector). Try doing that. I
keep 2 cards in a pocket, and any extras in a box, in the order of the
series (bottom right corner). That way I can just haul out the spares if
I need them, and its easy because I've already sorted them ahead of time.