Preheat oven to 350 degrees.
Melt butter in a small skillet over medium heat. Saute shallots until soft and translucent. Set aside.
Whisk together eggs, cream, salt and ground red pepper. Set aside.
Place phyllo cups in wells of mini muffin pan(s). Evenly divide shallots, cheese and spinach in cups. Pour egg mixture into cups until full. (You may have a bit of egg mixture left over.) Bake for 15 minutes. Serve warm or at room temperature.