From Martha Stewart's Cupcakes Book

makes 56 mini or 18 regular 

The Cupcakes:
1 1/2 cups all-purpose flour 
3/4 cup unsweetened Dutch-process cocoa powder
1 1/2 cups sugar 
1 1/2 teaspoons baking soda 
3/4 teaspoon baking powder 
3/4 teaspoon salt 
2 large eggs 
3/4 cup buttermilk 
3 tablespoons vegetable oil 
1 teaspoon pure vanilla extract 
3/4 cup warm water 

1. Preheat the oven to 350°F. Line mini muffin tin with paper liners. Whisk together flour, cocoa, sugar, baking soda, baking powder, and salt. With mixer on low speed, add eggs, buttermilk, oil, extract, and the water; beat until smooth and combined.

2. Spoon the batter into liners about two-thirds full. Bake approximately 15 minutes, or until tester comes out clean. Transfer tins to wire racks and allow to cool for 10 minutes; turn cupcakes onto racks and let cool completely. Cupcakes can be stored overnight at room temperature, or frozen up to 1 month in air tight containers.

3. To finish, use a paring knife to cut a cone-shaped piece (about 1/2 inch deep) from the center of each cupcake and throw away the pieces. Spoon 1 to 2 teaspoons warm Salted Caramel Filling into each hollowed-out cupcake. You will notice the caramel will sink into the cupcake a little, just fill it up a bit more. Sprinkle a pinch of sea salt over filling.

4. Use a pastry bag with a medium open-star tip (I used Wilton #1M) and pipe Dark Chocolate Frosting onto each cupcake, swirling tip and releasing as you pull up to form a peak. Garnish each cupcake with a pinch of sea salt. Cupcakes are best eaten the day they are filled and frosted. Store at room temperature in airtight containers - do NOT refrigerate. Enjoy!

Salted Caramel Filling
2 1/2 cups sugar 
2/3 cup water 
1 tablespoon light corn syrup 
3/4 cup heavy whipping cream 
2 1/2 teaspoons sea salt, preferably fleur de sel 

1. Heat sugar with the water and corn syrup in a heavy saucepan over high, stirring occasionally, until syrup is clear; clip a candy thermometer to side of pan and stop stirring.

2. Cook until syrup comes to a boil, washing down sides of pan with a wet pastry brush as needed. Boil, gently swirling pan occasionally, until mixture is caramelized and just reaches 360°F. Remove rom heat and slowly pour in cream; stir with a wooden spoon until smooth. Stir in sea salt.

Use immediately; if caramel begins to harden reheat gently until pourable.

Dark Chocolate Frosting
1/2 cup plus 1 tablespoon unsweetened Dutch-process cocoa powder
1/2 cup plus 1 tablespoon boiling water 
2 1/4 cups (4 1/2 sticks) unsalted butter, room temperature 
3/4 cup confectioners' sugar, sifted 
1/4 teaspoon salt 
1 1/2 pounds best-quality semi-sweet chocolate, melted and cooled

1. Combine cocoa and boiling water, stirring until cocoa has dissolved.

2. With electric mixer on medium-high, beat butter, confectioners' sugar, and salt until pale and fluffy. Reduce speed to low. Add melted and cooled chocolate, beating until combined and scraping down sides of bowl as needed. Beat in the cocoa mixture. 

3. Frosting can be refrigerated up to 5 days, or frozen up to 1 month in an air tight container. Before using, bring to room temperature and beat on low speed until smooth again.