Preheat the oven to 425°. In a heavy-bottomed saute pan melt the butter over medium heat. Add the onions and sauté until translucent, about 10 - 12 minutes. Add the flour and nutmeg; cook 2 more minutes, stirring occasionally. Add the milk and cook until thickened, about 5 - 7 minutes. Squeeze as much liquid as possible from the spinach and add the spinach to the sauce. Add 1/2 cup of the Parmesan cheese and mix well. Season to taste, with salt and pepper. Transfer the spinach to a large baking dish and sprinkle the remaining 1/4 cup Parmesan and the Swiss cheese on top. Bake for 20 minutes until hot and bubbly. Serve hot.