I made these last month for a 'wrap it up' themed potluck. I promised to make the best desert, and I think I made it happen. I made chocolate chip cookie dough wrapped in a cupcake! I borrowed the idea from a non-vegan blog, and made it work. Best of all though, is that with vegan cookie dough there isn't any fear or getting sick from raw cookie dough.
I made just under 3 dozen cupcakes. I used two batches of vanilla cupcake from the infamous Vegan Cupcakes Take Over the World, but replaced the granulated sugar for brown sugar. I intentionally underfilled the cups knowing that the cookie dough would take up quite a bit of room.
For the cookie dough, I used soy-free Earth Balance and Ener-G egg replacer in the recipe on the Ghiradelli bag. I only needed one batch of cookie dough, to fill all the cupcakes with small balls and make a dozen mini cookies as toppers. I used the frosting from Annie's Eats original recipe with 1 cup of earth balance and 1/2 cup of shortening.
Even though I froze the cookie dough balls for 2 hours prior to baking them in the cupcakes, they still seemed to cook a little. It's possible that a longer freeze might help, but you could also just fill the cookies after baking to not worry about it.
I highly recommend these! One of my even friends described them as life altering.