Well, I charge $1.50 & up for my standard cupcakes with just a nice size swirl of frosting. Fillings are an additional $.25/cupcake. The base price goes up depending on the cake flavor, the design, etc, etc.
For decorated cookies, I charge $1/inch with the typical price going between $3-$4/cookie. Same deal...more detail equals higher price per cookie.
For bakery cookies (chocolate chip, soft sugar, oatmeal, etc) I charge $2/4" cookie.
I also have a minimum order for most items so as not to have to mess up my kitchen for one cupcake or something 
! Mini cupcakes: 2 dozen, standard cupcakes: 1 dozen, jumbo cupcakes: 1/2 dozen, and muffin tops: 1/2 dozen. For bakery cookies, the minimum is a dozen as well. I haven't had the need to put a minimum order on the decorated cookies however since most people going that route want more then just a couple anyhow
...now if I was a stand-alone bakery, I would offer everything individually, but alas, I am not (yet 
)! HTH!
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