Preheat the oven to 175°C and line the muffin tin with 12 paper cupcake liners.
In a medium bowl whisk together the flour, cocoa powder, baking powder, and salt until well combined.
In a large bowl whisk together the sugar, milk, oil, eggs, and vanilla extract until smooth.
Add the dry ingredients to the wet ingredients and mix with a spatula just until no dry streaks remain.
Divide the batter evenly among the 12 liners, filling each about two-thirds full.
Bake the cupcakes for 16 to 18 minutes or until a toothpick inserted in the center comes out clean.
Remove the pan from the oven and let the cupcakes cool in the tin for 10 minutes.
Transfer the cupcakes to a wire rack and let them cool completely for at least 30 minutes.
While the cupcakes cool, beat the softened butter with an electric mixer in a medium bowl until creamy and pale, about 2 minutes.
Gradually add the powdered sugar, mixing on low until incorporated, then increase to medium speed until fluffy.
Add the heavy cream and vanilla to the frosting and beat until smooth and spreadable.
Transfer 3 tablespoons of the vanilla frosting to a small bowl and set aside for the penguin bellies and faces.
Melt the dark chocolate chips in a microwave-safe bowl in 20-second bursts, stirring between each, until smooth.
Mix the melted chocolate into the larger portion of frosting and beat until fully combined and chocolatey.
Spread or pipe a dome of chocolate frosting onto each cooled cupcake to form the penguin body.
Roll out the black fondant to about 3 mm thickness and cut 12 small oval shapes for wings and 12 round shapes for heads.
Roll out the white fondant and cut 12 smaller ovals for bellies and 12 small circles or teardrops for face patches.
Attach a white belly oval to the front of each cupcake by gently pressing it into the chocolate frosting.
Place one black fondant head circle on the top front edge of each cupcake, securing it into the frosting.
Add a white fondant face patch onto each head, pressing lightly to adhere.
Shape tiny triangles from the orange fondant and press one onto each face to create a beak.
Roll small balls of black fondant or use mini chocolate chips and press two onto each face for eyes.
Attach two black fondant ovals to the sides of each cupcake as wings, angling them slightly outward.
Shape small orange fondant ovals or wedges and place two at the base of each cupcake to resemble feet.
Refrigerate the decorated cupcakes for 5 to 10 minutes to help the fondant set before serving.