Yields about 5 dozen
For the brownies:
1 stick unsalted butter, cut into 3 pieces
4 oz. unsweetened chocolate, coarsely chopped
4 large eggs, at room temperature
1/4 teaspoon salt
2 cups sugar
1 teaspoon vanilla
1 1/4 cups flour
For the cream cheese topping:
6 ounces cream cheese (3/4 block), softened
3 tablespoons sugar
1 large egg yolk, at room temperature
1/2 cup semisweet mini chocolate chips
Heat the oven to 350º and line mini muffin tins with foil or paper liners.
Make the brownie batter: Combine the butter and chocolate in a small heatproof bowl. Microwave for 30 second intervals and heat, stirring frequently until the butter and chocolate are melted and smooth. Set aside.
With a stand mixer (use the whisk attachment) or a hand mixer, beat the eggs and salt in a large bowl on medium speed until very foamy, about 2 minutes. Continue beating while gradually adding the sugar. Beat until thick and pale, about 3 minutes. Scrape the chocolate mixture into the egg mixture, add the vanilla, and fold until the two mixtures are just barely incorporated. Add the flour and continue folding until just incorporated. Scrape the batter into a 1-gallon plastic storage bag. Squeeze out as much air as possible and seal.
Make the cream cheese topping: In a medium bowl, beat the cream cheese and sugar until smooth and creamy. Add the egg yolk and mix until blended. Pour in the chips and mix until blended, being careful not to break the chips. Scrape into a 1-quart plastic storage bag. Squeeze as much air as possible and seal.
Assemble and bake: Snip off one corner of each bag, to make a piping bag. Fill each lined muffin cup about two-thirds full with the brownie batter and then top with about 1 teaspoon of the cream cheese mixture.
Bake trays in the center of the oven until the brownies are puffed and a pick inserted in the brownie comes out just barely clean, about 20 minutes. Let the brownies cool in the trays on racks for 5 minutes before carefully lifting them to racks to cool completely. Be sure the tins are completely cool before lining and filling them with the remaining batters. Store at room temperature or freeze in an airtight container, separating the layers with waxed paper.