Swing by your local farmers' market to find heirloom varieties of yellow tomatoes in the fall. While you are there, pick up a few extra pounds to core and freeze whole so that you can make this soup throughout the winter. If you can't find yellow tomatoes, red beefsteak tomatoes will work just as well.
Preheat the oven to 350 degrees.
Lightly oil the yellow tomatoes. Place the tomatoes on a baking sheet and season with salt and pepper, to taste. Roast the tomatoes in the oven until the skins pop open and the flesh is fairly tender. Let cool to room temperature.
Place the tomatoes, all the reserved vegetable scraps, and the jalapeño in a blender and purée. Press the purée through a fine-meshed sieve. Season with salt, pepper, and vinegar, to taste. Add the lime juice.
In a bowl, combine all of the diced vegetables. Stir the vegetables into the purée or reserve the vegetables and use them to garnish the soup. Refrigerate the soup overnight to allow the flavors to develop. Serve the soup chilled, garnished with the cilantro.