Preheat oven to 350 degrees F. Place a paper cupcake liner in each cup of a standard muffin pan.
To make crust: In a bowl, combine graham cracker crumbs, sugar and melted butter until crumbs are moistened. Press crust into bottom of each muffin cup. Put 1 peanut butter cup into the center of each crust.
To make the filling: Beat cream cheese with a handheld electric mixer until fluffy. Add sugar, flour, and vanilla, beating well. Add eggs, 1 at a time, beating well after each addition. Spoon cream cheese mixture over peanut butter cups and graham cracker crusts. Bake until just set, about 20 minutes. Allow to cool completely before serving.