Combine ground flax and water in a small bowl; set aside. Whisk flour, baking powder, baking soda, and salt in a medium bowl. In a large bowl, mix applesauce, flax mixture, vanilla, honey, and yogurt until smooth.
Divide batter between muffin cups. Bake for 29-33 minutes, or until a toothpick comes out clean. Cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.