Preheat oven to 375 degrees Lightly grease large casserole dish.
Bring large pot of salted water to a boil.
In a large frying pan, melt butter over medium low heat. Add the onions and cook, stirring occasionally, until golden brown.
Once water comes to a boil, add cubed potatoes. As they begin to soften, about 5 minutes, add penne pasta. Cook, stirring occasionally, until potatoes are tender and pasta is just tender, about 7 minutes. Drain and gently rinse with cold water.
In a small bowl, season cream with salt and pepper.
Add 1/3 of penne and potatoes to the bottom of prepared dish. Evenly cover with 1/2 of grated cheese. Top with another 1/3 of penne and potatoes. Top with remaining cheese, then remaining penne and potatoes. Pour the cream over the layers. Evenly cover with caramelized onions.
Cover and bake in preheated oven until heated through and cheese is melted, 10-15 minutes.
Serve hot over applesauce.