Preheat the oven to 375 degrees F. Spray a baking pan with nonstick cooking spray and place the squash in the pan.
Heat 1 tablespoon of the butter in a medium skillet over medium heat. Add the onion and cook until tender and translucent, 6 to 8 minutes. Transfer the onion to the pan with the squash.
Return the skillet to the heat and add the remaining 5 tablespoons butter. Heat until the butter melts and begins to brown, 3 to 4 minutes. (The butter will begin to separate and sizzle. Take care to let it gently brown rather than burn. If the butter burns, throw it out and try again.) Stir in the sage. Drizzle the butter mixture over the squash and sprinkle with the salt and pepper. Use a wooden spoon to toss the mixture until the squash is evenly coated with the browned butter.
Bake until the squash is tender and beginning to brown around the edges, about 1 hour. Remove from the oven and increase the temperature to 400 degrees F. Top the squash with the crackers and cook until the crackers are nicely golden brown, an additional 20 minutes.