I store mine a couple of ways. The majority of my minis (over 1,000 of the little suckers) are stored in snap-lock bags in a couple of plastic storage containers. The minis in the various snap-lock bags are sorted into groups such as Orcs, Kobolds, Skeletons, Zombies, Underdark, Animals and Goblins.
My human, dwarf, elf, halfling and gnome minis are kept in a different storage container. Since there are a lot of these I have sorted them a little differently. The humanoids are sorted by race: Dwarves, Elves and Little People (Gnomes and Halflings). The humans are sorted into Sword & Board, Single Handed Weapon (No Shield), Two Handed Weapon, Two Weapons, Polearms, Exotic Weapons, Casters and finally Cultists.
In a third storage container (a flatter under-the-bed container) I keep all my Huge-sized minis as well as quite a few Large-sized minis.
Finally, I keep some other minis in some transparent Plano (Plano is the brand name) tackle boxes. Since they are transparent I can quickly look at them and see what minis are in each box. I have 4 tackle boxes in two different sizes. The smaller sized boxes fit my Medium-sized minis and short Large-sized minis. The larger sized boxes fit the taller Large-sized minis (although some Large-sized minis still don't fit, such as Frost Giant Jarl).
In one of the smaller sized tackle box I store the players' PC minis along with all of the minis that I expect to use in the next session or two. The other 3 boxes have mainly "monster" minis. These are mostly DDM Rares of various monsters like Dragons, Beholders, Efreeti, Shield Guardians and Ogre Magi. Most of them are minis that I found hard to put into a particular "category" for storage.
So there you go. My system is a little complicated, and it took quite a while to sort all the minis into various categories. However, since I have sorted them out finding the exact minis I need for a session has been a lot easier.
If there is one thing I would suggest, it is that you keep an inventory of the minis you have. Use an Excel spreadsheet or something similar. This will help you keep track of exactly what minis you have so that you don't accidentally order minis that you already have (not that I would do something stupid like that!
). And trust me when I say it is a lot easier to inventory them as you go along rather than after you have collected over 1,000 of them!
Olaf the Stout