Preheat oven to 350°F. Spray tops of 2 muffin tins with nonstick spray and line each cavity with cupcake liners.
In a 3-quart saucepan, combine water, cocoa powder, and butter. Melt over medium heat, whisking to moisten cocoa powder and prevent sticking.
Bring mixture to a low boil, then remove from heat.
Add vegetable oil, dark brown sugar, and bittersweet chocolate. Let sit for a couple minutes, then whisk until smooth.
Whisk in milk, vanilla, vinegar, eggs, and egg yolk until fully incorporated, about 2 minutes.
Sift flour, baking soda, and baking powder into a large bowl. Add granulated sugar and salt, then whisk to combine.
Carefully pour dry ingredients into the saucepan with the chocolate mixture.
Whisk gently until most lumps are gone, then whisk in sour cream until fully incorporated. Batter will be thin.
Use a 1/4 cup measuring cup to evenly spoon batter into 24 cupcake liners.
Bake for 14-17 minutes, or until a toothpick inserted in the center comes out clean and cupcakes spring back when pressed gently.
Remove from oven, gently press any misshapen cupcakes to even shape, then cool on a wire rack for 3 minutes.
Carefully remove cupcakes from tins and cool completely before frosting.
Frost with Creamy Chocolate Buttercream or preferred frosting.
Store unfrosted cupcakes loosely covered at room temperature up to 5 days or freeze for up to 2 months.