1. Preheat your oven to 350 F (175 C). Lightly spray a 12-cup muffin tin with cooking spray.

2. In a large mixing bowl, crack the 12 eggs. Add the milk, salt, and black pepper. Whisk vigorously until the egg yolks and whites are fully combined and slightly frothy.

3. Stir in the shredded cheddar cheese, diced bell pepper, diced onion, and the optional cooked ham or bacon into the egg mixture. Make sure all the ingredients are evenly distributed.

4. Carefully pour the egg mixture into each cup of the prepared muffin tin, filling each about three-quarters full.

5. Place the muffin tin in the preheated oven and bake for 20-25 minutes. The egg cups are done when they are set in the center, lightly golden brown around the edges, and spring back slightly when gently pressed. A toothpick inserted into the center should come out clean.

6. Once baked, remove the muffin tin from the oven. Let the egg cups cool in the tin for about 5 minutes before carefully removing them. Serve warm or allow them to cool completely for storage.