I use multiple cardboard cardboxes (ranging from 150 to 400 count sizes, so far), labeled in about 25 different categories. (E.g., monstrous humanoids, drow, dwarves, aberrations, et cetera.) I store the boxes on shelves, along with all Large models and some of the more impressive Mediums. If I need to take them somewhere, I can either pick out the ones I need and box them up, or throw a bunch of boxes into a larger box or bag.
It works really well, primarily because the miniatures are so light and nigh-indestructible.
Jeff