Preheat oven to 350. Line 24 muffin cups with cupcake liners.
In a medium bowl stir together flour, crushed graham crackers, and baking powder. Set aside.
In a large mixing bowl beat peanut butter and shortening with an electric mixer on medium. Mix well, then add in sugar until well mixed. Then add in eggs and vanilla. Alternate flour mixture and milk beating on low after each addition.
Spoon 1 rounded tablespoon of batter intot he bottom of each cupcake liner. Add 1 whole peanut butter cup to each cupcake. Spoon remaining batter into cupcake liners.
Bake about 18 minutes or until a toothpick comes out clean. (Cupcakes make have a slight indention)