Preheat oven to 350 degrees F (175 degrees C). Grease cookie sheets. Sift together the flour, baking soda and salt; set aside. In the microwave or in a bowl over a pan of simmering water, melt the chocolate and peanut butter chips, stirring occasionally until smooth. Set aside.
In a large bowl, cream together the butter, white sugar and brown sugar. Beat in the eggs one at a time then stir in the vanilla. Stir in the melted chips until well blended then stir in the sifted dry ingredients. Finally, fold in the chopped peanut butter cups. Drop by tablespoonfuls onto the prepared cookie sheets.
Bake for 10 to 15 minutes in the preheated oven. Allow cookies to cool on baking sheet for 5 minutes before removing to a wire rack to cool completely.
