The best replacement for cupcake is muffin.

The best alternatives to cupcake are rated as following:
★★★★★  muffin
★★  cake
★★  fairy cake
★★  cake cooking time
★  bun
★  muffin pan
★  donut
★  cosmetic warrior
★  cake recipes
★  wedding cake
★  muffin tin
★  cup cake
★  magdalena
  cake baking time
  regular cupcake
  thing-o-matic
  cupcake
  macaron
  muffin pans
  mini cupcake
  reprap
  ding dong
  buttercup

Your alternative for cupcake is not listed? Suggest!
Speaking about cupcake, one probably shouldn't forget about crossbones.

Other search terms related to cupcake and their ratings are:
★★★★★ crossbones
You have in mind a companion for cupcake and it is not yet here? Propose!



Google Trends

Scale is based on the average worldwide traffic of cupcake in all years. Click on graph for more.
cupcake
muffin
cake