Begin by heating your oven to 350F and prepping your muffin tin by giving it a good spray with non-stick cooking spray. Alternatively, you can grease them with butter or shortening. Then in a large bowl, whisk together your eggs, onion, salt, and pepper until well combined. Next, fill each muffin tin half full of the egg mixture. Then you can add your toppings, making sure not to fill past 3/4 full or your muffins will expand over their allotted space. When they are topped appropriately, bake them for 20 minutes or until a toothpick inserted into the middle comes out mostly clean (cheese can make them look not done in the middle).
Then remove from the oven and either: serve immediately, allow to cool completely before putting in an airtight container and storing in the fridge, or wrapping with press n seal and storing in the freezer. If you are storing them in the fridge or freezer, to warm simply unwrap, place on a plate and cover with a damp paper towel before microwaving for 20-30 seconds.