Cut the bagels into cubes. Arrange them on a baking sheet and toast them at 350 degrees for 3-4 minutes. Coat a 9x13 baking dish with nonstick cooking spray. Place the bagel pieces into the baking dish.
Place the eggs, cream cheese and half-and-half in a large bowl. Using an electric hand mixer, beat them together. There will still be chunks of cream cheese, which is okay. Stir in the smoked salmon, capers and chives.
Pour the salmon mixture over the bagels. Cover with plastic wrap and weigh down with another baking dish. Refrigerate overnight or at least 1 hour.
When ready to bake, preheat oven to 350 degrees. Unwrap the casserole and top with slices of Swiss cheese. Bake 40-45 minutes.
Cool at least 20 minutes before slicing into squares. Garnish with additional fresh chives and fresh ground black pepper, if desired.