Preheat oven to 375 F. Grease and flour a 12-cup muffin tin or line with paper muffin tin liners. Set aside. Make sure you really grease the muffin tin so that the brownies don't stick.
Melt chocolate and butter in a heavy saucepan over low heat, stirring constantly until melted and well-combined.
Remove from heat, and set aside.
In the bowl of a stand mixer, beat the eggs, sugars, vanilla, and salt on high speed 5 minutes, or until the batter is thick and creamy.
Reduce the speed to low, and mix in the melted chocolate until well-combined.
Stir in flour and cocoa powder just until combined.
Add chocolate chips. Stir in to combine. The batter should be the consistency of a thick brownie batter at this point.
Divide batter among muffin cups. They should be about ¾ full.
Bake 15-25 minutes. The brownies will be puffed and the top should be shiny and cracked. Bake toward the lower end of the baking time if you want fudgier middles and longer if you want a cakier brownie.
Let cool in muffin tin for 10 minutes, and then remove to a wire rack to finish cooling.
I've had good luck greasing the pan with baking spray that has flour in it. I've also had good luck using parchment paper liners.
Chocolate chips: I like to use bittersweet chocolate chips. If you like things sweeter, you can use dark chocolate or even semisweet chocolate chips.
Flour: Just like with regular brownies, using a light touch with the flour will help to keep the brownie bites fudgy. To measure the flour properly, stir or sift the flour to break it up, the lightly spoon it into the measuring cup and level.
I slightly underbake my brownies to keep those middles a fudgy. Since I underbake them, the middles fall a little as they cool, which makes the perfect little dip to set a scoop of ice cream in.
I've included a picture just above the recipe that shows the brownie bites more underbaked and the pictures above that show the brownie bites less underbaked to show the difference that baking times can make on the outcome.