Preheat oven to 350F. Set oven rack to middle position. Spray an 8x8 baking dish with nonstick cooking spray.
In a 12-inch nonstick skillet, add butter, olive oil, onion, squash, and zucchini. Season with 1 ½ teaspoons salt and ½ teaspoon black pepper. Cook over medium heat until the onions are translucent and the squash and zucchini are just barely still firm and start to caramelize, about 8 minutes. Stir frequently to evenly cook the vegetables.
Meanwhile, in a large bowl, whisk together sour cream, eggs, cayenne pepper, remaining ½ teaspoon salt, and cheese.
Add in cooked vegetables and gently stir together with a spatula. Pour into prepared pan. Set aside.
In a medium bowl mix all cracker topping ingredients until you get small uneven streusel-like crumbs. Evenly sprinkle topping over vegetables.
Bake until set, but the center just barely jiggles when touched, about 35 minutes.
Remove from the oven, let sit for about 5 minutes, and serve.