Preheat oven to 350 degrees F.
Using a biscuit cutter, cut 4-inch diameter circles from large tortillas (you may want to microwave the tortillas for 10-15 seconds to soften them up to allow easier cutting).
Brush tortillas on each side with a small amount of melted butter, and press into each cup of a 12-cup muffin tin, forming a small bowl.
Bake tortilla cups for 10 minutes, or until slightly golden brown; remove and set aside when finished.
While cups are baking, melt 1 tablespoon of butter in a large skillet over medium-high heat; saute onions and jalapeno peppers until the onions are soft and translucent.
Add eggs, cajun seasoning and pepper into pan, and scramble until eggs are cooked through, but not completely firm, as they will be going into the oven.
Toss tomatoes and cheese in egg mixutre until cheese is slightly melted.
Spoon egg mixture into pre-baked tortilla cups and bake for an additional 10 minutes.
Garnish with fresh cilantro or chopped green onions and serve.