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Make the filling: Beat together the cream cheese, granulated sugar, and egg until smooth. Stir in the chopped chocolate pieces. Set aside.
Make the cupcakes: Adjust the rack to the center of the oven and preheat to 350°F (175°C). Butter a 12-cup muffin tin, or line the tin with paper muffin cups.
In a medium bowl sift together the flour, cocoa powder, baking soda, and salt.
In a separate bowl, whisk together the brown sugar, water, oil, vinegar, and vanilla.
Make a well in the center of the dry ingredients and stir in the wet ingredients, stirring until just smooth.
Divide the batter among the muffin cups, leaving just a couple spoonfuls behind in the bowl.
Spoon a couple tablespoons of the filling into the center of each cupcake, dividing the filling evenly.
Spoon any remaining chocolate batter back over the cream cheese center, if you plan to marble the tops.
Use a butter knife inserted only about ½-inch into the cupcake to swirl the batters together decoratively.
Bake for 25 minutes, or until the tops are slightly golden brown and the cupcakes feel springy when gently pressed.