Preheat the oven to 350°. Spray 6-7 muffin cups with vegetable spray and set aside.
Heat the olive oil in a medium skillet over medium-high heat. Add the bell pepper and onion. Saute until softened and onions are slightly translucent. Add the ham and cook for an additional 1-2 minutes. Remove from heat, stir in the tomatoes and set aside.
In a medium bowl whisk together the eggs, salt and pepper. Stir in 1/2 cup smoked gouda and the ham mixture. Ladle the egg mixture into the prepared muffin cups. Sprinkle the reserved gouda over the omelette cups. Bake for 15-17 minutes or until the eggs are set.
Turn the oven from bake to broil. Brown the omelettes for 1-2 minutes until golden. Run a sharp knife around the edge of each omelette and transfer to a serving platter. Serve.
To Freeze:
Let the omelettes cool to room temperature. Line a tray with parchment paper and arrange the omelettes on the tray. Freeze the omelettes until solid. Transfer the omelettes to a freezer-safe baggie.
Reheat the omelettes in the microwave for 1-2 minutes at 50% power, checking halfway through.