Preheat oven to 350°F. Coat a 24-serving mini-muffin pan with cooking spray. Evenly divide the quartered tomatoes among the muffin cups, and top each with 1/2 teaspoon feta or goat cheese.
Crack eggs in a large, glass measuring cup or bowl. Add milk, pesto, salt and pepper; whisk to combine. Divide mixture evenly among muffin cups.
Bake at 350°F for 10 minutes or until the muffins are set. Cool for 2–3 minutes; remove the muffins from the pan and cool on a wire rack.