I've seen others use really nice clear containers for individual cupcakes but finding a source has not been easy. I'm sure many of what I have seen were from local manufacturers in the countries of those I saw using them (like the people from China and Japan who had clear containers for their cupcakes).
Here is one of the best sources I could find here in the states:
http://www.pjpmarketplace.com/servlet/the-3254/Sundae%2C-Ice-Cream%2C-Dessert%2C/Detail?zmam=9154908&zmas=1&zmac=7&zmap=345090
This site does deal in large bulk orders but they do carry some really great stuff and is worth checking out.
If there is anybody who knows of another place to purchase individual clear covered containers that will fit cupcakes please share.
There's a couple box companies that offer the bakery boxes with cupcake inserts...would love to get some of those but as they sell them by the 100 count, I'd need 2 or 3 people to go in with me on them 
This place has some good ideas for cupcake holders, cake holders and other bakery packaging. Thell sell by the unit.
http://www.plasticcontainercity.com/Cupcake-Containers-Muffins.htm
i use http://www.brpboxshop.com and get cute pink boxes with inserts for a 12 pack and a single cupcake. they are a bit pricey but i do charge customers for the individual gift boxes. i just tack it on to their final cupcake price. i think they may be a bit pricey but i got tired of searching through sites and just ordered.
ashley
what about papermart:
http://www.papermart.com/index/index_retail_box_plastic.htm
I haven't ordered from them, but I've wanted to, their stuff looks neat.
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