Most places charge anywhere from $2.50 and up per cupcake depending on the embellishments.I charge $2.50 for a simple BC swirled cupcake.If I am doing gumpaste or small flowers on each cupcake the price goes up from there.Once the bride decides what stlye she wants you can charge her accordingly.
If you are adding chocolate shells or gumpaste seashells then I would most definetly charge anywhere from $3.00 and up....Cupcakes are very tedious and time consuming so don't let it fool yah!!
Your Welcome..Everyone needs help and guidance....
$999. I price less than Charm City in order to remain competative. 
Seriously, though here's ALL you need to take into consideratoin:
1) cost of ingredients including shipping or gas + wear and tear on your vehicle to go to the store
2) cost of utilities used while making and decorating: electricity, gas, water.
3) how long it took you x how much you want to make per hour
If you know that, then you can figure out how much to charge for ANY cake.
I hate cupcake wedding cakes. A lot more work than a regular cake, IMO. Remember you are having to pick each one of those buggers up a couple of times EACH (X 60 cupcakes). Also make sure you have a plan in place for transporting them - they fall over and get messed up easy if not properly restrained!! I am in the $2.50 - 3.00 each range too, but take the advice of the PP's and make sure you aren't shorting yourself.
To me cupcakes should be close to your regular cake prices if they are filled and decorated on top.
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