Preheat oven to 375F. Butter standard muffin tins. Finely grate the zest from the oranges, removing only the bright orange portion of the peel. You should have about 1/4 cup of zest. Combine the zest, 1/4 cup of the sugar and the water in a small saucepan. Stir over medium heat for about 2 minutes, until the sugar dissolves.
Add the butter and stir until melted, about 1 minute more. Set aside. In a medium stir and toss together the flour, baking powder, baking soda, salt and the remaining 1/4 cup sugar. Set aside. In a large bowl whisk together the eggs, yogurt, milk and reserved orange mixture until smooth. Add the combined dry ingredients and stir just until blended.
Spoon into the prepared muffin tins, filling each cup about three-quarters full. Bake until a toothpick inserted in the center of a muffin comes out clean, 15-20 minutes. Cool in the tins for 3 minutes, then remove.