Oddly, I'm also in the midst of inventorying and re-classifying my 2500+ minis collection. Is it something in the air?
I use
THESE. I have about 40 categories (e.g., "Weapon-and-Shield Warriors," "Arcane Casters," "Dwarves," and so on), so I have four of these.
I use colored plastic slide-out bins, 14 or 15 of them, for my Large-based minis.
My Huge-based minis sit on shelves that circle my game room, and my Gargantuan- and Colossal-based minis have their own shelf, up high and out of the way.
Going the card-house route was the smartest choice I ever made, in terms of storage. I can have a suitable mini for pretty much any encounter in 10 seconds, and I can have a specific mini in 30 seconds.
I also use an Excel spreadsheet to track my inventory (including things like what's stored where). I'm just now wanting to learn how to link an image to a cell, so I can click on, say, "Cleric of Order" and have the image of that mini show up in the worksheet.