The food questions keep coming from Jenny and Friends.

Near Mikes (North End) there is another:
Modern Pastry makes a better canolli if that's what you want.

Lulu’s Bake Shoppe pretty much specializes in cupcakes and is a 1 minutes walk from Mikes (and modern). All are located on Hannover in the NE.

There's another in the NE, Bova's. The cupcakes and pastries aren't amazing, but it's actually a 24/7 shop, so if your craving hits at 2a, you can get a cupcake there.

Other neighborhoods:
Portugeuese cupcakes at O Cantinho Café in cambridge. Sorta like a flan cupcake.

South End has:
The Buttery, which makes a Cream Cheese topped cupcake.

Flour, which I think now has a waterfront location, is an organic, green, "fancy" cafe and pastry shop. The website has gorgeous food photography if you like that kind of thing (like me). My favorite for how much the chefs care about the food. Similar to SF's acclaimed ACME company.

I've got many others, but those are my favorites. Finale is very good, too, but can get loud and crowded if its the right nights. It all depends what neighborhoods you want to stick too and how far through 20 degree air you are willing to travel to feed your need.

PM if you need more info.