Combine the cookie crumbs and melted butter. Place a spoonful of crumbs in 24 cupcake liners. Press down firmly. Set aside.
In a mixing bowl, beat the cream cheese, sugar, and vanilla until creamy. Add the eggs, sour cream, and flour and beat again.
In a microwave safe bowl, combine the chocolate chips and shortening. Heat for 30 seconds and stir. Repeat until melted. Let cool slightly. Pour into cream cheese mixture and beat until creamy. Spoon into prepared cupcake liners. Bake at 350* for 22 minutes. Let cool in pan for 3-4 minutes, then remove to wire rack to cool completely.
In a mixing bowl, beat the cream cheese and peanut butter until creamy. Add the cool whip and beat with the wire whisk attachment until creamy. Place spoonfuls on top of cooled cheesecake and spread out. Top with Reese's Peanut Butter Cups. Makes 24 cupcake cheesecakes. Keep refrigerated in a sealed container.