In a large pot, bring water and salt to a rolling boil. Add the broccoli and cook until it is crisp tender, about 5 minutes.
In a small sauce pan, melt the butter and whisk in the flour to form a roux. Turn heat down to low.
Drain the broccoli, reserving 1 cup of the water.
Whisk the reserved water into the roux and bring to a boil over medium heat. Simmer until thickened, about 3 minutes. Remove from heat and stir in the nutmeg, pepper, ¾ cup Parmesan cheese and all of the Monterey Jack cheese.
Place the broccoli in a shallow baking dish. Pour cheese sauce over and top with remaining 1/4 cup Parmesan cheese and the Panko bread crumbs.
Bake for 15 minutes at 350°F and broil on low for about 5 minutes until browned on top.