Pre-bake your pie shell until lightly browned. You can do this in advance.
Preheat the oven to 375.
Peel and chop the tomatoes. Separate the flesh from the juices and reserve the juices.
Heat the oil in a skillet and saute the chopped onion.
Add the tomatoes and spinach (or zucchini) and cook on med/low until the juices are gone. I usually add more of the tomato juice and reduce it again to intensify the tomato flavor. If you do not get this pretty dry it will be too wet for the quiche and you'll have a runny quiche.
Place the milk, eggs, nutmeg, thyme and salt and pepper in a bowl and whisk until eggs are incorporated.
Sprinkle a thin layer of cheese on the bottom of the pie shell. Add the tomato and spinach (or zucchini) and spread evenly over the cheese. Add the rest of the cheese.
Gently pour the wet ingredients over the layers in the pie shell. If you are using bacon sprinkle it on now.
Bake until a knife inserted in the center comes out clean. It will probably take 45-60 minutes. It depends on how cold your ingredients were. I usually cover it loosely with foil half way through to prevent the crust from over browning.