To prepare Chocolate Cake, preheat oven to 350 degrees. Combine cocoa and 2 cups boiling water in a large heatproof bowl, stirring until blended and smooth; cool completely. Beat butter with a mixer until creamy; gradually add sugar, beating until blended. Add eggs, 1 at a time, beating until blended after each addition. Combine flour and next 3 ingredients; add to butter mixture alternately with cocoa mixture, beginning and ending with flour mixture. Beat at low speed just until blended after each addition. Stir in chocolate extract.
Place paper baking cups in 2 (12-cup) muffin pans, and coat with cooking spray; spoon batter into cups, filling two-thirds full. Bake for 12 to 15 minutes. Cool in pans on wire racks 10 minutes; remove from pans, and cool completely.
To prepare Chocolate Ganache, cook cream in a heavy nonaluminum saucepan over medium heat, stirring often, just until it begins to steam (do not boil); remove from heat. Place chocolate in a glass bowl. Slowly add hot cream to chocolate, beating with a whisk until chocolate melts and mixture is well blended. The mixture will thicken as it cools. Makes about 2 cups.
Fill each cupcake with Ganache. To fill: Insert the end of a wooden spoon or dowel into the center of the cupcake to make a hole. Fill a zip-top plastic freezer bag with filling or frosting. Use scissors or kitchen shears to snip about 1/4 inch from one corner of the bag; insert bag into the hole in the cupcake. Squeeze gently until filling comes to the top of each cupcake.
To prepare Peanut Butter Frosting, beat butter and peanut butter at medium speed with an electric mixer until creamy. Gradually add half of powdered sugar, beating at low speed until blended. Add 1/4 cup cream, beating until creamy. Add remaining powdered sugar, beating until blended. If necessary, add more cream, beating at high speed 2 minutes or until creamy. Makes 3 cups. Frost each cupcake using metal tip number 12.
Drizzle each with warm Chocolate Ganache, and top with half of a peanut butter cup.