Halve onions from top to bottom. Resting on the cut side slice thinly into half circles. Measure out 6 cups. Melt the butter in a large heavy skillet over medium heat; when foam subsides add the onions. Cover and cook, over medium low heat, until wilted, about 15 minutes. Uncover and continue cooking over medium heat, stirring often and adjusting heat so that onions brown slowly, until the onions are a dark golden brown and very tender, about 20 minutes. Stir in the chopped thyme, salt and pepper.
Preheat oven to 350 degrees. Select 6 (5-ounce) custard cups; brush generously with softened butter. Arrange in a 13 by 9-inch baking pan. Set a kettle of water on to boil. Combine the milk and cream in a saucepan and heat until small bubbles appear around the edges. In a large bowl whisk the eggs and egg yolks until blended. Slowly add the hot milk, whisking gently until blended. Place a strainer over a large measuring cup with a pouring spout and strain the custard. Using a tongs distribute distribute the Sauteed onions evenly among the 6 custard cups (they should be about 1/4 filled). Add the custard, distributing evenly. Run a knife through the custards so that the custard will seep through the layer of onion.
Place the baking pan in the oven and carefully pour hot water into the pan until it is 1-inch up sides of the cups. Bake until custards are lightly browned and set, about 25 minutes. Remove the pan from the oven and using a spatula and protecting your hand with a pot-holder remove the custard cups from the water to a wire rack. Serve warm or at room temperature. Can be made ahead and reheated in the microwave or wrapped in foil and reheated in the oven.