Preheat oven to 350 degrees F. Cut squashes in half lengthwise and scoop out seeds and strings. Bake cut side down in ½-inch of water until tender, about 40 minutes. While squashes are baking, prepare the stuffing.
In a skillet melt the butter and saute apples and onion for 10 minutes or until both are very tender. In a large bowl combine apples and onion with raisins, brown sugar, cinnamon, and cheese. Place cooked squashes on a cookie sheet and divide apple stuffing evenly among cavities. Bake at 350 degrees F for 20 minutes or until apples are soft and cheese is melted. This dish, which can be prepared ahead, is great for holiday entertaining.