Preheat the oven to 350 degrees F.
Wash 2 of the three summer squash and cut off the stem end. Slide it lengthwide so that you have two long halves. Using a spoon, gently and carefully scoop out the seed cavity, discarding seeds.
Place halves of the summer squash, cut-side up, on a baking sheet and bake at 350 for 20 minutes.
Peel the remaining summer squash. Diced the stem end into fine small piece and discard the rest, using as much of the seed end as you can without including seeds or stringy bits.
Dice the onion and cut the cherry tomatoes in half.
In a large saucepan, place onions and olive oil, then gently heat until the onion is translucent, about 5 minutes. Add squash and sautee another 2-3 minutes, then add the tomato halves and sautee 5 more minutes.
Remove the squash from the oven. Spoon the squash, onion, and tomato mixture into the cavities of the squash. Return stuffed summer squash to the oven and bake for another 20-30 minutes or until squash is completely tender. Remove, serve with salt and pepper and other herbal seasonings of your choice.