Preheat oven to 350F/180C. Line 30-32 mini muffin cups with liners. Set aside.
Make the ganache first: In a medium heat-proof bowl, place chocolate and heavy cream. Melt the mixture in the microwave in 20-second intervals, stirring between each interval, until melted and smooth. Alternatively, you can set the bowl over a saucepan of simmering water, stirring occasionally. Cover the bowl and leave to cool until it has reached room temperature and thickens. It should be ready by the time the cupcakes are able to be frosted.
To make the brownies: In a large heat-proof bowl, place chocolate and butter. Melt mixture in the microwave in 20-second intervals, stirring between each interval, until melted (or set bowl over a saucepan of simmering water, stirring occasionally). Add sugar and whisk until combined. Add eggs, one at a time, and whisk just until combined. Add vanilla extract and stir. Sift flour and salt over the chocolate mixture and fold, using a rubber spatula, until combined and smooth. Do not over mix.
Divide batter between cupcake liners, filling them 3/4 full. Bake for about 10 minutes, until a toothpick inserted into the center of the cupcake, comes out with a few moist crumbs. Be careful not to over bake as this will make the brownies dry. Transfer to a wire rack and let cool for 10 minutes before removing from pan. Once cupcakes have cooled and the chocolate ganache has thickened, frost cupcakes.
Store cupcakes in an airtight container in the refrigerator for up to 3 days. Allow to reach room temperature before serving.