Preheat the oven to 350ºF and line a 12-cup muffin tin with silicone or paper liners. (Or grease the cups very, very well to prevent sticking.)
In a large bowl, beat together the eggs, salt, and pepper, then set it aside.
Fill the 12 muffin cups with your fillings of choice. If you'd like to make all 4 variations in one pan, use only 1/4 of what is called for above for each filling option. I like to fill each muffin cup nearly to the top with veggies, so consider the quantities above a suggestion. You can use as much or as little as you'd like to.
Pour the egg mixture over the top of the veggie fillings, filling each muffin cup. Place the pan in the oven to bake until the eggs are fully cooked, about 20 to 25 minutes. You'll know they are done when the centers have risen out of the pan. The egg muffins will puff up quite a bit when they are in the oven, but they will shrink down as they cool.
Allow the muffins to cool for at last 5 mintues before serving them warm. Leftovers can be stored in the fridge in an airtight container for 3 to 5 days. Serve them warm or cold. I like to reheat them in the oven at 350ºF for 8-10 minutes when I want to serve them again.