How to Make It
In a large skillet, heat 2 tablespoons of the olive oil. Add the onions, garlic and a generous pinch of salt and cook over moderate heat, stirring occasionally, until just softened and starting to brown, about 8 minutes. Scrape the onions and garlic into a large bowl.
Wipe out the skillet and heat 1/4 cup of the oil in it. Add the eggplant and thyme and cook over moderate heat, stirring occasionally, until the eggplant is tender and lightly browned, 8 to 10 minutes. Scrape the eggplant into the bowl with the onions. Repeat with the red pepper, zucchini, yellow squash and tomatoes, cooking each vegetable separately in 1 tablespoon of oil with a generous pinch of salt until just tender and lightly browned, 5 to 7 minutes per vegetable. As they are cooked, add the vegetables to the bowl of onions and eggplant. Stir in the chopped basil and lemon juice and season with salt and pepper.
Preheat the oven to 350°. Spread the goat cheese in the bottoms of 2 small baking dishes (about 1 quart each). Spoon the ratatouille on top, cover with foil and bake for about 25 minutes, until hot. Top with more basil. Serve warm with chips and crackers.