In a large mixing 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 mixing bowl until blended. Add egg and salt; mix well. Fold in the chocolate chips. Drop by tablespoons into the center of each cupcake. Sprinkle with nuts.
Bake at 350°F for 25 to 30 minutes or until a toothpick inserted in the cake and not the filling comes out clean. Cool for 10 minutes before removing from pans to wire racks to cool completely. Store in the refrigerator.