Preheat oven to 350 degrees. Spray a min muffin pan (24 tins) with non-stick cooking spray.
Combine the cracker crumbs and melted butter. Divide crumb mixture among the prepared mini muffin cups and press down firmly. Bake for 7 – 8 minutes. Remove from oven and set aside.
In a large skillet over medium heat, heat the oil and add the chopped onion. Cook the onions until very soft and starting to brown, about 10 minutes, stirring occasionally. Squeeze all the liquid out of the spinach, add to the onions along with the salt, pepper and nutmeg and cook, stirring, for 30 seconds. Divide the mixture evenly on the cracker crumbs. Divide the shredded cheese on top of the spinach mixture.
Whisk the eggs and milk together and spoon into the muffin cups; do not fill all the way. Top with the roasted red pepper slivers and bake until set and browned, about 20 minutes.