For warhammer I use magnets under each miniature and my movement trays are lined with a metal plate so the minis stay locked in position on each movement tray. For a case I use a large plastic bin divided up into blocks with foamboard dividers. Then I can put each movement tray in each compartment. The box costs very little to make. Here's a link to a picture of one of the boxes, but without the movement trays in place.
http://www.netmdc.com/~longfang/Subp...iature_Box.htm
Here's how I make quick and cheap magnetic movement trays:
http://www.netmdc.com/~longfang/Subp...ic%20Bases.htm
For 40K I use Sabol army trays. You can get foam inserts thick enough to fit any vehicle and customize your case to fit your army.