Preheat oven to 400 degrees. Place muffin liners in a 12 standard-size muffin pan.
In a large mixing bowl combine the dry ingredients; flour, ground flax, baking powder, baking soda and sugar. Add in yogurt, melted butter and milk. Stir until thoroughly combined, creating a smooth, stiff batter. Gently fold in additional ingredient options, then divide batter equally spooning into the muffin cups.
Bake for 15-20 minutes, or until tops are golden. Transfer to cooling rack. Serve warm or at room temperature, store remaining muffins in an air tight container.