Heat the oven to 350°F and line three one-dozen capacity (five if you have them) mini muffin tins with foil or paper liners.
Make the brownie batter:
Combine the butter and chocolate in a small heatproof bowl. Set the bowl over simmering water or in a microwave and heat, stirring frequently with a rubber spatula, 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. With a large rubber spatula, scrape the chocolate mixture into the eggs, 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 heavy-duty zip-top 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 with a wooden spoon until smooth and creamy. Add the egg yolk and mix until blended. Pour in the chips and mix until blended. Scrape into a 1-quart zip-top bag. Squeeze out as much air as possible and seal.
Assemble and bake:
Snip off 1/2 inch from one corner of each bag. Fill each lined muffin cup about two-thirds full with the brownie batter and then top with about 1 tsp. of the cream cheese mixture.
Bake the three 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 trays on racks for 5 minutes before carefully lifting the liners out of the tins and transferring 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.
Photo: Scott Phillips