Preheat oven to 350F.
In a large skillet, saute the onions in the ¼ cup butter over medium heat until tender.
Layer ½ the onion mixture in bottom of a 8x8 baking pan.
Cover with 1 cup Swiss cheese.
Top with 3/4 cup saltine crumbs.
Add remaining onions in a layer and top with remaining cheese.
In a bowl, combine the eggs, milk, and seasonings.
Pour over onion layers.
Melt 3 tablespoons butter and mix with remaining cracker crumbs.
Spread over top of casserole.
Bake at 350F for 20-25 minutes or until bubbly and the topping is golden brown.