In a medium bowl, zest ½ teaspoon orange rind. Add ¼ cup fresh orange juice from 1 orange. Section remaining two oranges over bowl; set aside.
Season salmon fillets with ½ teaspoon salt and ¼ teaspoon black pepper. Place olive oil in large, oven proof skillet over medium-high heat. Add salmon, top side down, and cook for 5 minutes. Remove fish from pan and set aside. Add onions and cook for 3 minutes. Pour orange juice from bowl into skillet – holding orange sections to be added later. Add orange sections, tomatoes, capers, ½ teaspoon salt and ¼ teaspoon black pepper; cook for 2 minutes, stirring occasionally.
Add salmon, browned side up, on top of tomato mixture. Place skillet in oven and bake at 400° for 5 minutes or to desired degree of doneness.