I go all the way back to Harbinger, and to original-release Mage Knight before that. Plus, Star Wars Miniatures on the side. Let me assure you, I know about quantity. ^_^
I only use the Plano tackle boxes for Medium or smaller PFB minis. I've got a couple of larger tackle boxes for the 4e-era D&D Minis, and then a tall set of plastic drawers for the 3.5-era minis. And then larger boxes for Large or Huge minis. The Star Wars minis have their own set of drawers, plus a large box for the big stuff. The Mage Knight stuff is mostly in two big boxes, sorted by era (original vs. 2.0).
Ahh... right now mine are sorted by monster type (so Good outsiders are in one box, evil outsiders in another, PC races in another, monstrous humanoids in another, etc). This was to make it easier to find a certain monster quickly when prepping for a game. Maybe I'll have to re-think that organization.