I made cupcakes in ice cream cones for the Kids Against Dumb Stuff costume party. There are a few ways to do it, but I like this way the best.
I use regular size cupcake tins and line them with paper cupcake liners, then pour the cupcake batter into each cup to about 2/3 full. You don't want to have too much batter in the cup or it will ooze out the sides, but you'll need enough so that it rises up into the cone when baking.
Place the open end of the ice cream cones on top of the batter, gently pressing so they fit snugly. If you press too hard they'll break! Oh, I used a boxed cake mix.
Bake as directed on the box for cupcakes.
This is what they look like before baking
This is when they come out of the oven. You can see what happens with too much batter, a few of them burst out the sides and tilted the cones. That's not a problem because you'll be icing them anyway, and ice cream cones don't have to be perfect. When cool, remove the papers and decorate your way.
EXTRA: You can also make them by pouring batter directly into the cone then baking, but you can't get them to stand up in a standard cupcake tin without support. That's why you would need one of the baking racks shown below. The racks can also be used if you're traveling with them. I know from experience these cupcake cones do not travel easily without a rack.