For filling, in a small mixing bowl, beat cream cheese and 1/2 cup sugar until smooth. Beat in egg and 1/2 teaspoon salt until combined. Fold in chocolate chips; set aside.
In a bowl, combine the flour, cocoa, baking soda, and remaining sugar and salt. In another bowl, whisk the water, oil and vinegar; stir into dry ingredients just until moistened.
Fill paper-lined muffin cups half full with batter. Drop filling by heaping tablespoonfuls into the center of each. Bake at 350° for 24-26 minutes or until a toothpick inserted in cake comes out clean. Cool for 10 minutes before removing from pans to wire racks to cool completely.
For frosting, in a large mixing bowl, combine confectioners' sugar, cocoa, butter, milk and vanilla; beat until blended. Frost cupcakes; sprinkle with pecans. Store in the refrigerator. Yield: 20 cupcakes.