I shipped cookies this past week (some about 1000 miles, the others 3000 miles).
I sent about 6 dozen cross cookies to my sister-in-law for my nieces communion - 1000 miles. For those, I put them in throw away tins (about 9x13, I think), beacuse they didn't have to be individually packaged. I tried to make it so that they wouldn't move around much, but weren't too tight fitting. I put wax paper between the layers and only did 3 layers deep in each tray. then I covered it with plastic wrap and wrapped the whole thing in bubble wrap. then I put that in a box (fairly tight fitting, and I filled in any extra room with stryofoam peanuts). I edned up with 4 boxes, so I put all of those boxes into another large box and padded them in well. They said that they all got there fine!
The ones that I sent across the country were for a thank you gift. they were wrapped individually and then put in a shirt box (padded with that paper stuff on the top and the bottom). Then I put the shirt box inside of a strudy cardboard pizza box (unused and inside out) and filled in any extra space with packing material. I haven't yet herad how those made it...