Preheat the oven to 350 degrees F.
Combine the flour, cocoa, baking soda and salt in a medium bowl. Set aside.
Cream the butter and sugars together in a large bowl with an electric mixer until fluffy. Add the peanut butter, vanilla and eggs and mix on low. Stir in the flour-cocoa mixture until just mixed. Fold in the chocolate chips, peanut butter chips and peanut butter cups and stir with a wooden spoon.
Drop a heaping tablespoonful of dough onto baking sheets, leaving 2 inches between each cookie to allow them to spread. Bake until set, but still a touch soft inside, 8 to 10 minutes. Cool for 2 minutes on baking sheet, then transfer cookies to wire rack to cool completely.