The best thing I have found is black packing foam. Cut blocks about an inch wide, then cut out a notch to cradle the aircraft, one up front, one in the back. For smaller models (1/72) a cradle up front and just a slit to slip the tail in(upside down). For much larger models, cut a support block for each wing to keep it from rolling. Don't be affraid to put some upside down, for some this is required and easier, especially if they're loaded up with ordnance.
My 1/32 A-10 has seen 3 trips to shows in this box, not one bit of damage.
When I move from KS to MI, I had 8-9 big shipping boxes with 3-4 layers in each one. Packed the bottom layer, then used styrofoam block to set the next cardboard shelf on, pack that layer, more blocks, shelf, and so on. I had anywhere from 15 to 20 in each box.
These are on the second "shelf" of a smaller box.
I always cut the cradles a little tight, just to keep this where they belong. I have never had any problems with packing them this way.
Oh yeah, use plain old elmers glue for the foam.