Preheat the oven to 350°F. Fill a cupcake pan with cupcake liners and set it aside.
Mix the flour, cocoa powder, salt and baking soda together in a bowl.
In a stand mixer (or with a hand mixer), cream together the butter and sugar until light and fluffy, about 3 minutes.
Add eggs, one at a time, while mixing, then add sour cream. Beat until well blended.
While still mixing, pour in half the dry ingredients then half the stout, then vanilla extract, then remaining dry ingredients, then remaining stout. Mix just until combined, do not over blend.
Fill the cupcake liners with the batter to 3/4 full. Bake for 17-19 minutes, until a toothpick inserted in the center comes out clean.
Remove from the oven and cool completely on a cooling rack.
Once the cupcakes are cool, use a knife or apple corer to remove a small chunk of cake from the center.