Preheat oven to 350 degrees Fahrenheit. Coat a 13 x 9 inch baking dish with cooking spray. Gather your ingredients.
Place onions in a large bowl. Sprinkle with thyme, parsley, garlic salt, oregano, mustard, and cayenne pepper; toss gently to coat. Arrange evenly in prepared baking dish.
Arrange butter evenly over onions, and sprinkle with Cheddar and Gouda. Cover with aluminum foil, and bake in a preheated oven until onions are soft and sides are bubbly about 40 minutes.
Remove foil. Bake at 350 degrees Fahrenheit until top is golden, about 30 minutes.