Heavily grease two muffin tins with nonstick spray or oil. Set aside.
Whisk all the eggs in a big bowl or in a food processor.
Add the green onion segments, zucchini slices, red peppers, and bacon to the food processor and pulse in 1 second intervals until the ingredients are finely chopped but NOT smooth. If it is not chopping evenly, spoon out the chopped food and finish pulsing the rest. Add all of this mixture to the eggs.
Add the spinach into the processor and finely chop. Add this to the eggs as well. Add the salt and pepper. Combine with a whisk.
Using a 1/4 measuring cup, fill the muffin tins. Bake for 20-25 minutes or until the middle is set. Don't overcook! The egg cups will shrink down significantly once you take them out of the oven. As long as the center is set when you take them out, you can rest assured that they are baked all the way.
If you are freezing these, wait for them to cool, then wrap them individually in plastic wrap and put them all in a Ziploc bag. Seal and freeze.
When you want to eat one, unwrap it, discard the plastic, and place on a folded paper towel on a plate in the microwave. Heat for about 1-2 minutes, or until the center is warm. Don't overheat it or you will get rubbery eggs.