I've never had to deal with more than 2 dozen cupcakes and I'm not sure how to transport that many. Thanks in advance.
I have never had to drive very far with my cupcakes but when I have alot of them I use the foil turkey roasting pans that you can buy at Walmart or any grocery store (cost about $2.50-$3.50 per pan) to put them in. They come with a cover so you can stack them and I usually can get about 20-25 regular sized cupcakes in a pan. If you do stack them you would want to put some of that non skid drawer liner stuff in between the pans so they dont slide off each other. I have had my pans for years and use them over and over! 
This question was recently part of another post. And it was very helpful to me. Buy a few of the clear plastic underbed storage boxes. I think they hold about 70-75 each . The trick is to put your un-iced cupcakes in the box and ice them in the box. That way you don't have to handle them too much or put them in the box with the icing soft. Good luck!
The under-bed storage box sounds like a great idea. I have used the cardboard shipping boxes that strawberries come in. They stack, and are tall enough to accommodate cupcakes with tall decorations/frosting. I was able to get 48 in a box, BUT, these had minimal decorations, and I was able to squish them in.
Here's a photo:
http://christinascakes.shutterfly.com/pictures/323
An excellent tip, regardless of the system you use, is to put rubberized shelf liner on the bottom of each box. This will help with the sliding.
Here is another method that would work well with cupcakes that have a lot of frosting:
http://www.wilton.com/forums/messageview.cfm?catid=8&threadid=143263&STARTPAGE=1&CFID=181028127&CFTOKEN=57008694
Wow well look at how we learn something new everyday. Thanks for that link to the wilton discussion. That is a great method. I have delivered up to 750 mini cupcakes to events in 14" sealed cake boxes without any toppling but this is really a smart idea in that link. I used to feel like I was wasting 10 cake boxes every time just to carry cupcakes to an event because icing would touch the sides of the boxes and I would never be able to re-use them for anything else.
For standard size cuppies I really like the under the bed boxes, I think I got about 65 each in mine? For mini's, I have a bunch of lids from the paper boxes that I have hot glued 1oz plastic shot glasses in (the kind you make jello shooters in!) and they are the perfect size to safely carry mini's. I can get at least 50 in one of the lids.
Thanks for the help everyone. I may use the aluminum foil method because I hate when my cupcakes get smooshed together.
I just did a 250 cupcake transport for a friends wedding this weekend. I used Kiwi boxes from Costco (they are high enough for a 1M swirl and any cake toppers). I covered them with Ziploc XXL bags (they come in 3 per box). The good thing was that since I used the same boxes they were able to be stacked.
To make sure they did not move, I only put 40 cupcakes per box, and in between each row, I stuffed it with tissue paper, or newspaper. HTH. They did not suffer any damage (except for 1 because the hubs had to slam on the breaks due to someone elses bad driving)
I love the kiwi box idea....
I have several large plastic "under the bed" type containers. They are as wide as both my arms held out to my sides...if that makes sense? I use them for everything.
You have to be a little careful when you got through doorways because you have to turn to the side. But, other than that, they are great.
The kiwi boxes would probably be easier to handle for set up though. I have to set my container on two chairs next to each other and bend down slightly.
I pack tight enough so they don't move at all, but not so tight that they are mushed. I guess it depends on how your ice your cupcakes. The tissue paper makes sense. I'll try that myself next time...
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