Preheat oven to 160°C. Line 18 holes of two ⅓-cup (80ml) muffin pans with paper cases. Combine the chocolate and 1 cup (250ml) water in a small saucepan over low heat. Cook, stirring, for 5 mins or until the chocolate melts and mixture is smooth. Remove from heat. Set aside to cool.
Use an electric mixer to beat the butter and brown sugar in a bowl until pale and creamy. Add eggs, 1 at a time, beating well after each addition. Add the flour and cocoa powder. Stir until just combined. Stir in chocolate mixture. Divide evenly among paper cases. Bake for 20 mins or until a skewer inserted in the centres comes out clean. Set aside in the pan for 5 mins before transferring to a wire rack to cool completely.
Meanwhile, combine the cherry and caster sugar in a small saucepan over low heat. Cook, stirring occasionally, for 5 mins or until the sugar dissolves and cherry releases its juices. Increase heat to medium-high and bring to the boil. Cook for 5 mins or until the syrup thickens. Set aside to cool.
Reserve half the cherry mixture in a small bowl. Place the remaining cherry mixture in a blender and blend until smooth.
Use a clean electric mixer to beat extra butter in a bowl until very pale. Gradually add the icing sugar, in batches, beating well after each addition. Add cherry puree. Beat until well combined.
Use a small knife to cut a 3cm-wide, 2cm-deep cone from the centre of each cupcake. Spoon the reserved cherry mixture into the holes.
Transfer buttercream to a piping bag fitted with a 1cm fluted nozzle. Pipe over the cupcakes. Top with whole cherries.