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Melt the butter in a saucepan, add the onions and saute on low heat until soft and fragrant. Stir in the salt, pepper and nutmeg and turn off the heat. Stir in the wilted spinach and set aside to cool.
Whisk together the milk, mustard and eggs in a large bowl. Add the cooled onion and spinach mixture and the cubed bread. Mix well. Cover and refrigerate for at least 4 hours and preferably overnight.
Preheat the oven to 350 degrees F. Grease jumbo muffins tins well.
Mix the Gruyere, ham and Parmesan into the strata mixture. Divide the mixture among the muffin tins and bake until the stratas are set and the tops of the strata muffins are browned, 30 to 40 minutes. Let cool for 10 minutes, and then remove from the tins.