I have waaay to many and I will only get more. I organize them into these groups (placed in huge ziplocks bags, clearly marked then placed in a huge tub). The cards are stored in plastic sleeves like baseball cards).
My categories are designed around the monster types/subtypes of the Monste Manual:
Aberrations
Animals
Constructs
Dragons - Metallic, Chromatic, Other
Magical Beasts
Outsiders - Outer Planes, Inner Planes
Ooze (only 1 guy in this group unfortunately)
Plants
Vermin
Undead - Greater, Lesser
Then I have a few separate sections for these guys:
Iconic - Regular guys and the Psionic Iconic
Celestials
Fiends - Devils; Fiends - Demons; Fiends - Other
Eberron specific
Greyhawk specific
Forgotten Realms specific - Good, Evil, Iconic
All generiic humanoids and monstrous humanoids get their own ziplok bag organized by race (all gnolls in one bag, all gnomes in another). With large numbers of a race, such as humans, I break them down into Good, Evil and Neutral groups.
- Ed