What is a good way to keep your miniatures organized and safe? I am currently using a shoe box, and the miniatures are all thrown together. The pieces I have a lot of are pretty easy to get to, but the pieces I only have one or two of (like a dragon) sometimes get pretty buried – or worse, broken.
(Inspired by What's an organized storage solution for Dungeon Tiles?)
My wife made me a storage solution for Christmas out of stackable ornament boxes with egg-crate foam added to the bottom of each compartment. She also pulled the dividers out, but you could go either way on that. It's pretty freaking awesome, especially because it's easily expandable and cheap. You can also just fill up one compartment with minis you know you'll need and just take that.
I use a variety of boxes. The black/yellow ones I purchase at Harbor Freight Tools ($8).
It has removable boxes that I can mix and match between cases.
The clear ones I purchase at Big Lots ($12). 
They have removable trays and I can mix and match the top four I want to bring to a game. 
The top also is a great place to stage minis, hold dice and even roll dice.
I use a bunch of IKEA Krus boxes. I leave the separators in for small and medium minis, and pull them out for a couple of boxes of larger minis. Right now, I have a box for undead, one for humanoids, one for elementals, and so on. They stack nicely and don't take up too much room.
I find that sewing or fishing lure boxes can make good cases and some even come with adjustable plastic dividers. For added protection you can get some foam to keep it from banging around in transport.
Depending on the size of your items, you might want to look into a bead organizer box. I used to carry my HeroClix in a plastic bead sorting box. The compartments tend to be on the smaller side though, so it isn't ideal for something as large as a dragon. Still, I found it a great way to carry around normal size figures without them banging into each other and getting chipped.
I found a few online similar to what I had for my Clix: 12 slot box, 32 slot box, 8 slot box with bigger containers.
My son plays a lot of Warhammer 40K and while their cases are okay for carrying miniatures I think they are expensive. The solution I arrived at is to buy aluminium cases from your local DIY store and then fill it with fabric/furniture foam from a sewing shop. I buy the foam in different thicknesses – 5mm and 30mm – and cut dedicated shape out of the 30mm foam.
That gives you a custom case for half the price of a typical GW case. Alternatively if you want to spend some pennies a lot of my friends say good things about KR Multicase.
I've always used Chessex boxes for my typical 25mm miniatures. For larger miniatures you will want to look into customizable boxes such as the Army Transport bags and trays.
A fishing tackle box with a bit of foam padding works good as well, and is inexpensive compared to tupperware storage drawers.
If you need to move a small number of miniatures relatively regularly then Impact do good foam lined, pre cut, carrying cases.
A few years back I purchased a Gamer's Satchel from Charon Productions.
I was able to carry a single foam tray of miniatures, a few D&D books, and my binder of notes. The satchel should be able to hold two or three trays of miniatures. I purchased additional trays to store additional miniatures at home. The trays are nice since they won't harm the paint on the minis. The edges can also be cut out for larger pieces.
Charon's phone support was great in helping me find what I needed. They do offer several other options of carrying cases.
Something seems to be wrong with their links at the main site, but I had better luck by choosing the "Shopping Cart" link at the top and browsing their products.
Obviously not an ideal or scalable solution by any measure, but I keep the handful minis I have in a small dice bag, which resides in the larger bag that actually contains my dice.
I use Bead/Jewelry plastic organizer boxes lined with foam. Trying to cut up the foam is a pain but the lid is very secure. Plus it has the virtue of being able to put two side by side in an old style milk crate.
Try plant starter trays from home improvement or garden stores. They are way cheap and can be stacked and labeled. They come in sizes too.
Tool boxes or fishing tackle boxes are usually very good. They are designed to be portable and hardy and often have plenty of subdivisions of just about the right size for miniatures, so if you find the right one you shouldn't need to do any conversion work beyond perhaps creating some foam inlays to protect your miniatures from rough handling.
