In a large bowl, combine the flour, sugar, cocoa, baking soda and salt. In a bowl, whisk the eggs, water, oil, vinegar and vanilla. Add to dry ingredients; mix well.
Pour into 18 greased or paper-lined muffin cups. For filling, beat cream cheese and sugar in another large bowl. Add egg and salt; mix well. Fold in the chocolate chips. Drop by tablespoonfuls into center of each cupcake. Sprinkle with nuts.
Bake at 350° for 25-30 minutes or until a toothpick inserted in the center of the cupcake (not the filling) comes out clean. Cool for 10 minutes before removing from pans to wire racks to cool completely. Store in the refrigerator.