1 Preheat oven to 400° F.
2 Sauté onions and garlic: Using a large oven-proof pan over medium high heat, sauté onions in 2 tablespoons of olive oil until they begin to soften, about 5 minutes. Add garlic and reduce heat to low.
3 Sauté zucchini: While the onions and garlic are cooking over low heat, heat 2 tablespoons of olive oil in 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.
4 Sauté the remaining veggies: Cook the yellow squash in the same manner as the zucchini. 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.
5 Season: 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, along with thyme, bay leaf, rosemary, and the vegetable stock. Stir well.
6 Cook the veggies in the oven: Place the pan in a 400°F oven, and cook, uncovered, for 30 minutes. Alternatively, you can cook them on the stovetop on low heat for 30 minutes.
7 Prep the tomatoes: If using fresh tomatoes, boil water in a saucepan. Remove the stems from tomatoes, and crisscross the bottoms with a knife. Plunge the tomatoes into boiling water for a minute or two, until skin starts to fall away. Rinse in cold water and remove the skin.
Cut tomatoes in half lengthwise, remove seeds, chop coarsely, and set aside.
8 Make a glaze: After the vegetables have been in the oven for a half hour, remove from oven, drain vegetables in a colander set over a bowl to catch the juices. Clean browned bits (if any) off the 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.
9 Combine cooked vegetables with chopped tomatoes: 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.
10 Serve: Remove the bay leaf, and season to taste with salt and pepper. 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.