Preheat the oven to 375°F.
Generously oil or coat a 12-cup muffin pan with nonstick cooking spray and set aside. Divide the bread cubes evenly and place into the muffin cups
Whisk together the eggs, squash, cheddar cheese, Parmesan cheese, and bacon bits in a large bowl until well blended. Using a 1/4-cup measuring cup, pour the egg mixture into each of the bread-filled muffin cups.
Bake until golden brown, about 22 minutes. Cool slightly, remove from muffin tins, and serve with maple syrup or ketchup as desired.
Variation: For a sweeter alternative, replace the 3 slices of whole wheat bread with 3 slices of whole grain cinnamon raisin swirl bread, and replace the bacon bits with 2 tablespoons of brown sugar.