Preheat oven to 400*F. Cut four sheets of aluminum foil into 45 centimeter lengths.
Toss zucchini, squash, sliced shallot and garlic together with two tablespoons olive oil. Season with salt and pepper to taste and divide among four sheets of foil, placing veggies in center of foil.
Season the salmon fillets with salt and pepper then place one fillet over each layer of veggies on foil. Toss together tomatoes, shallots, lemon juice, remaining olive oil, capers, season with salt and pepper.
Divide tomato mixture over salmon fillets. Place the thyme and basil on top of package. Wrap sides of foil inward then fold up ends to seal. Place on a rimmed baking sheet and bake in preheated oven until salmon has cooked through, about 25 - 30 minutes. Carefully open foil packets and serve warm.