Preheat the oven to 350 degrees . Grease a 12-cup muffin pan and fill each cup halfway with bread cubes. Top each with a cream cheese slice.
In a small saucepan, heat the olive oil over medium heat and add the ham, scallion whites and a pinch of pepper. Cook, stirring, until the scallions are tender, about 5 minutes. Stir in the half-and-half and bring just to a simmer before removing from the heat.
In a medium bowl, whisk together the eggs and thyme, then whisk in the warm half-and-half mixture. Fill the muffin cups with the egg mixture and bake until puffed and golden around the edges, about 15 minutes. Let cool for 5 minutes, then run a knife around the edges and invert onto a cooling rack.
Drizzle the tomato slices with olive oil, top with the scallion greens and season with salt and pepper. Serve with the mini casseroles.