Little Tomato-Pesto

8 ripe tomatoes: 4 medium red, 2 medium-large yellow, 2 medium-large green, about 3 pounds
2 medium yellow onions
6 tablespoons pesto, homemade or store-bought

1. Preheat oven to 325 degrees F.
2. Wash tomatoes and dry thoroughly. Cut red tomatoes in half horizontally. Lightly coat 8 custard cups with nonstick vegetable spray and place tomatoes in them cut side up.
3. Peel onions and cut each into 12 thin slices. Top each tomato with 1 onion slice. Spread 1 teaspoon pesto over each onion slice.
4. Cut each yellow tomato into 4 thick slices. Place a slice on top of each pesto-smeared onion slice. Top with another onion slice. Spread 1 teaspoon pesto on top.
5. Cut each green tomato into 4 thick slices. Place on top of onion. Top with another thin slice of onion. Spread with 1/4 teaspoon pesto.
6. Place custard cups on a rimmed baking sheet. Bake for 1 1/2 hours, carefully pouring off liquid every 30 minutes, and pressing down on napoleons with a spatula. Collect all juices in a small bowl.
7. When finished, let napoleons cool for a few minutes. Place juices in a small nonstick skillet and cook over high heat until juices are syrupy-reduced to about 1/2 cup. Add kosher salt and freshly ground black pepper to taste. Turn napoleons out onto a platter. Pour reduced juices over top and serve.