Preheat oven to 350°F.
Grind the flax seeds on high in a blender until they become a powder. Add soymilk and blend for another 30 seconds or so. Set aside.
In a large bowl sift together flour, cocoa, baking soda and salt.
In a seperate large bowl cream together oil, sugar/stevia, and applesauce. Add the flax seed/soy milk mixture and mix well. Add the vanilla.
Fold in the dry ingredients in batches. When it starts to get too stiff to mix with a spatula, use your hands until a nice stiff dough forms. Add the chocolate chips and mix with your hands again.
Roll dough into 1 inch balls and flatten into a disc that's about 1 1/2 inches in diameter. Place on an ungreased cookie sheet about an inch apart.
Bake for 10 minutes. Remove from oven and let cool for about 5 minutes, then set them on a wire rack to cool completely.
For chocolate chocolate chip cherry cookies, replace 1 teaspoon of the vanilla with almond extract, and replace 1/2 the chocolate chips with dried cherries.
For chocolate nut cookies, replace 1 teaspoon of the vanilla with a nut extract (almond, walnut, what have you) and replace the chocolate chips with 1 1/2 cups chopped nuts (hazelnuts, almonds or walnuts all are good).