You can pretty much fill a cupcake with anything you want; frosting, jam or jelly, mousse, candy, curd, ganache, and more. The Cuisipro Cupcake Corer ($5, Williams Sonoma) can make filling cupcakes a cinch. Make sure your cupcakes are completely cooled and then twist the corer into the cupcake (a guard indicates how deep to cut). Pull corer out and push plunger to remove the core. Easy! Then you just fill your cupcake and frost.
You can find a lot of cupcake filling recipes online as well as other ways to core a cupcake. Click here, here, or here for some recipes and tips or do a search for "filling cupcakes."
Also, check out the DC Cupcakes girls favorite cupcake and filling combos.