1. Preheat oven to 350°F and spray a muffin tin with non-stick spray.
2. In a large bowl, whisk together eggs and onion. Season with salt and pepper, to taste.
3. Add egg mixture halfway up into each tin of a greased muffin tin.
4. Divide the three topping combinations into 4 muffin cups each.
5. Bake for 20 minutes.
Note: Let the egg muffins cool completely, then wrap individually in plastic wrap and pop them in a freezer-safe zip-lock bag. They will last for up to 2 months. You can eat them on their own, or pop each one into an English muffin!