Preheat oven to 350°F. Line muffin tins with paper liners.
In a large bowl, whisk together the flour, brown sugar, cocoa, baking powder, baking soda and salt, breaking up any lumps of brown sugar and cocoa. Add the milk, oil, eggs and vanilla and whisk to combine; add the coffee and stir until well blended and smooth.
Divide the batter among the cups, filling them 3/4 full, and bake for 25 minutes, or until the tops are springy to the touch. Cool completely.
Meanwhile, simmer the cherries, sugar and cornstarch (if you like, stir the sugar and cornstarch together first in a small bowl to get rid of lumps) over medium heat until bubbling and thickened. Remove from heat and let cool.
With a sharp knife, cut a small piece out of the top of each cupcake. (I cut in a circle with the knife pointed in, so you end up with a little cone shaped chunk of cake.) Fill each cupcake with a small spoonful of filling, then replace with the chunk of cake (you may have to break off the pointy end to accommodate the filling).
Whip the cream with the sugar and vanilla until stiff peaks form. Spoon into a larger zip-lock bag, snip a bigger piece off one corner and pipe out over the cupcakes. Top with cherries, chocolate shavings or chocolate trees.