Preheat oven to 350 degrees F (175 degrees C). Spray 24-count mini muffin cup pan with non-stick spray.
Mix flaxssed and water and allow to sit five minutes before using.
In large mixer bowl, beat oil, sugar, brown sugar, flaxseed mixture, and vanilla until well blended. Add applesauce, blend well.
In a separate bowl, stir together flour, cocoa, baking soda, if desired. Add to liquids, blending well. Stir in chocolate chips. Fill muffin cups 3/4 full with batter.
Note: I only used 20 of the rather small mini muffin cups in my pan. They don't rise much, and come out flat on top. Bear this in mind when filling.
Bake at 350 degrees F (175 degrees C) for 15-18 minutes or until wooden pick inserted in center comes out almost clean. Cool in pan on wire rack for 5 minutes, then carefully remove to wire rack. Sprinkle muffin tops with confectioners' sugar, if desired. Serve warm.