Hands down by far my absolute favorite cupcake bakery is CRUMBS. They have amazing flavors and HUGE cupcakes. Snickerdoodle, Oreo, Chocolate Chip Cookie, Hostess Cupcake, Twinkie and Double Chocolate are my favorites. Reasonable prices (as far as cupcakes go) and you get alot of cake in your cup.
The number two honor belongs to Sprinkles. A west coast founded cupcake which was my all time favorite until I discovered CRUMBS. Sorry Sprinkles. I will say Sprinkles does have the best Red Velvet cupcake to date but gets outnumbered by CRUMBS' diverse flavor menu.
A cupcake / skull logo! Are you joking? I ABSOLUTELY LUV IT! And the cupcakes are bad either.