Melt the butter substitute in a saucepan over medium heat. Once melted, stir in the graham cracker crumbs and remove from heat. Stir in the peanut butter and sugar, mix well. Evenly divide the mixture among the 12 paper cups, about 2 tablespoons each.
In another saucepan, combine the chocolate chips and milk and stir over medium heat until the chocolate has melted. Spoon the mixture over each individual peanut butter cup evenly, and top with chopped nuts. Chill in the refrigerator for at least 2 hours.