This is the most basic version of a dish that is found all over the Southeast in meat 'n threes. It varies widely, but always contains squash, onions, and crackers; sometimes you'll find cheese, mayo, breadcrumbs, pimentos, or bell peppers mixed in, too. My grandmother wrote this recipe and it has been served at our restaurant for decades. —HMMessinger
Bring a large pot of water to boil and add 1 tablespoon kosher salt per quart. Chop squash into 1-inch pieces and boil until tender, but not mushy, about 5 to 7 minutes.
Melt 4 tablespoons butter in a pan and sautée onions until soft, 5 to 7 minutes. Set aside to cool.
Drain squash well and rinse under cold water. Set on a dish towel to dry. Preheat oven to 450° F and butter a 9- by 11-inch baking dish.
Whisk together milk, eggs, and 1 teaspoon salt. Add 1 to 2 teaspoons sugar if you are using poor quality (or out of season) squash.
Layer squash and buttered onions in a baking dish and pour milk mixture over it. Top with cracker crumbs (I am partial to cheese crackers, but Ritz crackers are the traditional choice), and drizzle remaining 2 tablespoons butter over top.
Bake for 20 minutes, or until custard is set. Let cool about 10 minutes before serving.