Preheat the oven to 425 degrees F.
Melt the butter in a heavy-bottomed saute pan over medium heat. Add the onions and saute until translucent, about 15 minutes. Add the flour and nutmeg and cook, stirring, for 2 more minutes. Add the cream and milk and cook until thickened. 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 baking dish and sprinkle the remaining 1/2 cup Parmesan and the Gruyere on top. Bake for 20 minutes until hot and bubbly. Serve hot.
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