Heat oven to 425 degrees F. Coat 2 large rimmed baking sheets with nonstick cooking spray.
Spread zucchini, squash, red pepper and onion in a single layer on the prepared baking sheets; coat generously with nonstick cooking spray. Sprinkle vegetables with 1/2 teaspoon each of the salt and pepper. Roast at 425 degrees for 30 minutes, stirring halfway through, or until edges are browned. Remove from oven and transfer vegetables to a bowl.
Pulse mushrooms in a food processor until finely chopped. Heat olive oil in a large nonstick skillet over medium-high heat. Add mushrooms to skillet. Cook, stirring, for 6 minutes or until all liquid has evaporated. Reduce heat to medium; stir in garlic and remaining 1/2 teaspoon each salt and pepper; continue to cook 1 minute.
Add butter to skillet and cook until melted. Add flour and cook 1 minute, stirring. Add milk and nutmeg to skillet and increase heat to medium-high. Bring mixture to a boil. Reduce heat to medium and simmer for 8 to 10 minutes or until thickened, stirring occasionally. Remove skillet from heat and stir in 2 tablespoons of the parsley and all the basil.
Meanwhile, bring a large pot of salted water to a boil. Cook noodles according to package instructions, about 9 minutes. Drain, rinse with cold water and set aside.
Coat a 13 x 9 x 2-inch baking dish with nonstick cooking spray. Stir together Fontina and Parmesan. Spread 1/2 cup mushroom sauce into bottom of baking dish, then place 3 noodles in dish. Pour another 1/2 cup sauce over noodles, then sprinkle 1/3 of the vegetables and 1/2 cup cheese mixture over sauce. Repeat layering twice. Top with three noodles, pour the rest of the sauce over top and sprinkle with the remaining cheese.
Cover dish with nonstick aluminum foil and bake at 425 degrees for 20 minutes. Raise heat to 500 degrees, Remove foil and cook for another 12 minutes or until browned. Sprinkle with remaining 2 tablespoons parsley and let stand 15 minutes before serving. Makes 8 servings.