Method 1 Preheat oven to 400° F.
Using a large oven-proof pan over medium high heat, sauté onions in olive oil until they begin to soften, about 5 minutes. Add garlic and reduce heat to low.
While the onions and garlic are cooking over low heat, put 2 tablespoons of olive oil in a another frying pan over high heat. As soon as oil starts to smoke, quickly add enough zucchini cubes all at once to cover the bottom of the pan. Keep on cooking over high heat, stirring, until zucchini is lightly browned on all sides. Remove zucchini cubes, and add them to pan with the onions.
Working in batches, repeat this process until all of the zucchini cubes have been cooked. Do the same with the yellow squash. Make sure to add a little olive oil between each new batch. Continue with the bell peppers, then the eggplant cubes, adding the browned vegetables to the onion pan as soon as they are cooked.
When all the vegetables (except the tomatoes) are browned and in the pan with the onions, increase the heat to high and stir, making sure they don't stick to the bottom of the pan. Add salt to taste, thyme, bay leaf, and rosemary, the vegetable stock, and stir well. Place in oven, uncovered, for 30 minutes. Alternatively you can cook them on the stovetop on low heat for 30 minutes.
If using fresh tomatoes, boil water in a saucepan on stove. Remove stems from tomatoes, and crisscross the bottoms with a knife. Plunge into boiling water for a minute or two, until skin starts to fall away. Rinse in cold water and remove skin. Cut tomatoes in half lengthwise, remove seeds, chop coarsely, set aside.
After the vegetables have been in the oven for a half hour, remove from oven, drain vegetables in a colander set over a bowl. Clean browned bits (if any) off bottom of pan with a paper towel. Return any liquid to the pan and reduce to a thick glaze over medium high heat. Keep on adding juices to the pan as they run out of the vegetables into the bowl.
When all the juices have been reduced, return vegetables to the heavy pan. At this point the ratatouille should be moist and shiny, with very little liquid. Turn heat off. Add the chopped tomatoes and cover. If serving as a warm side dish, let the ratatouille stand for 10 minutes, just enough to "cook" the tomatoes. The ratatouille can be served at room temperature or refrigerated and reheated the next day.
When ready to serve, remove the bay leaf, and season to taste with salt and pepper. Serves 6-8.