Score skin of fish in a diamond pattern. To prepare snapper marinade, combine 1 cup lime juice, water, orange juice, and 1 tablespoon salt in an extra-large plastic bag. Add fish; seal and marinate in refrigerator 20 minutes, turning bag once. Remove snapper from bag; discard marinade.
Preheat oven to 425°.
To prepare spice rub, combine green onions and the next 9 ingredients (green onions through garlic cloves) in a food processor or blender, and process until smooth. Spread spice rub evenly over both sides of fish. Place fish on a rack coated with cooking spray.
Place tomato wedges, onion wedges, and wine in a shallow roasting pan, and place rack with fish over vegetables in pan. Cover with foil; bake at 425° for 30 minutes. Uncover; bake an additional 45 minutes or until fish flakes easily when tested with a fork. Remove skin from top side of fish; discard skin. Remove tomato mixture from pan; serve with fish.