In a deep, heavy-bottomed pot, sauté onions and garlic in the olive oil until translucent. Add eggplant, zucchini, squash and green peppers and stir well. Cook over medium heat, covered, for 10 minutes, lifting lid frequently to stir. Remove lid and add tomatoes. Simmer over medium heat for 10 minutes. Transfer tender vegetables to a sheet pan and place in refrigerator until cool. Once vegetables have cooled, place them in a large mixing bowl. Add basil; salt to taste. Add a splash of balsamic vinegar if desired.
Using a 1½-ounce scoop, place one scoop of goat cheese on the bottom of each baked pastry cup. Push down with back of scoop. Place pastry cups on a baking pan and bake for 6 minutes. Remove from oven and top with ratatouille and fresh-cracked pepper. Can be served warm or at room temperature.