Preheat the oven to 375°F. Spray a nonstick regular-size (not jumbo) muffin tin with cooking spray, or grease with vegetable oil and a paper towel. Place the muffin tin on a baking sheet.
In a large saute pan, cook the bacon over medium heat until brown and crisp, about 8 minutes. Drain on a paper towel-lined plate. Increase the heat to medium high and add the shallot. Cook for 2 minutes or until translucent. Add the spinach (you may have to do this gradually, depending on how big your pan is), stirring constantly and cooking until bright green and wilted. Remove from the heat and season with salt and pepper to taste. Stir in the bacon.
In a large bowl (preferably with pouring spout), whisk together the eggs and egg yolks. Season generously with salt and pepper.
Divide the spinach-bacon mixture into the bottoms of the 12 muffin cups. Carefully pour (or ladle) the egg mixture over the spinach, filling each muffin cup until nearly full. Add a few crumbles of goat cheese to each cup (make sure to use it all) and finish with a sprinkling of red pepper flakes.
Carefully place the baking sheet in the oven. Bake for 15 to 17 minutes or until the tops of the frittatas are puffed up like little souffles. Turn the oven up to broil and cook for an additional 2 minutes to create a nice golden color on top.
Let cool for a couple of minutes then, using a small knife, cut around the edges of each frittata to remove them from the pans. (NOTE: Soak the pan immediately in soapy water to remove any egg remains.) Serve hot or at room temperature.