Bring a large saucepan of water to a boil. Cook the gnocchi until they float, 3 to 5 minutes or according to package directions. Drain.
Meanwhile, melt butter in a large skillet over medium-high heat. Cook until the butter is beginning to brown, about 2 minutes. Add shallots and zucchini, squash and cook, stirring often until softened, 2 to 3 minutes. Add tomatoes, salt, nutmeg and pepper and continue cooking. Stirring often until the tomatoes are just starting to break down, 1 to 2 minutes. Stir in Parmesan and parsley. Add the gnocchi and toss to coat. Serve immediately.
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