Place semisweet chocolate and butter in a microwave-safe bowl. Heat at half power in 30-second increments until the butter has melted and the chocolate melts when stirred. Stir until smooth. Set aside to cool.
Preheat oven to 350°F (175°C). Grease 12 standard-size muffin cups or line them with paper liners.
Add the eggs, sugar, and vanilla to the cooled chocolate mixture. Use a mixing spoon or an electric mixer to mix until thoroughly combined.
Stir in the flour and salt, mixing just until combined. Stir in the nuts.
Fill each muffin cup about half full. Place about a tablespoonful of flavored chips on top of the batter. Cover with the remaining batter, filling each cup almost full.
Bake 30 to 35 minutes, or until a pick inserted into the center comes out with moist crumbs. Cool in the pan on a wire rack.
To store: Transfer your brownie cupcakes to an airtight container and store them at room temperature for 3 to 4 days, or freeze them for up to 3 months. Let them thaw at room temperature before serving.