Hot out of the oven, clafoutis are light, puffy, and soufflé-like, but as they cool, their tops fall and their consistency becomes quiche-like.
Preheat oven to 375°F. Coat 12-cup muffin pan with cooking spray.
Beat eggs in bowl. Gradually whisk in flour. Stir in milk, sour cream, thyme, salt, and pepper. Divide half of batter among muffin cups. Bake 10 minutes.
Place 3 tomato halves in each muffin cup, round-side up. Pour remaining batter over top, and sprinkle with pine nuts and cheese. Bake 22 minutes more, or until tip of knife inserted in center comes out clean. Cool 1 minute, then unmold with knife or thin spatula. Serve warm.