When you have this many miniatures to store and transport, it becomes a fairly expensive proposition.
I found some really good cases a long time ago, which have since been discontinued, of course. They are made by Akro-Mils, who makes a lot of the plastic cases you see in stores. These are from the Akro Logic Multicase line. Basically they are a stackable case with removable bins. They come in two different depths, about 2" and about 3.5". The shorter size is good for most vehicles. The taller size holds Ogres all the way up to Mark 6.
Since these cases spend the vast majority of their time on my shelves, I just put foam in the bottom of each bin and line up the vehicles side by side. I have driven to game conventions with these cases and have only had a few instances where the vehicles got bounced out of place. I don't like having them rub up against each other though, so I am going to try to figure out a way to add some padding to keep things in place better.