Preheat oven to 350 degrees. Place squash in a large saucepan with onion. Add enough water to cover; bring to a simmer. Cover, and cook until squash is tender, 10 to 15 minutes. Drain, and mash slightly in a colander, pressing to remove as much liquid as possible; transfer to a large bowl.
Add 1/2 cup cracker crumbs and 1 tablespoon butter to squash. Season with coarse salt and ground pepper; mix well. Transfer to a shallow 8-inch square baking dish. Sprinkle with remaining crumbs; dot with remaining tablespoon butter. Bake until golden, 25 to 30 minutes.
I was not very happy with this recipe. It turned out squishy and bland for me.
My three year old who won't eat any vegetables loves this recipe. I've also mixed in zucchini when I was short of yellow squash.