Don't forget to incorporate your labor costs into the equation - they are the lion's share of the cost structure of a decorated cookie!
To price product in my bakery, I used typical recipe/food costing methods of the food biz. I first built up the full cost of making the product, including labor (using standard time to make the thing x cost of my labor, i.e., $ per hour). Then I added a 30% to 50% margin (50% margin = double the cost to get the price) to cover other overhead costs associated with running the bakery AND to make a profit.
There are lots of programs out there that can help with product pricing, but the key thing (which only you can do) is developing the standards or know-how to gauge how long something takes to make (per unit) from start to finish, starting with mixing the dough to packaging the cookies up, if relevant.
This is just one example of recipe costing software, which I can't vouch for (as I've never used it), but shop around. If you want a more reliable recommendation for software, I can check with some chef friends of mine who do this everyday: http://www.accuchef.com/