I vary it depending on what I feel like and what I find on sale. The things to look for are good quality, distinctive flavor, and good melting characteristics. Mixtures of different ones, e.g. asiago, mozzarella and a little Parmesan, can be nice. Most people use sharp cheddar, and for reasons best known to themselves prefer a yellow cheese to a white one.
Thomas Jefferson popularized the dish in America. He grew fond of it while ambassador to France, brought back an Italian pasta machine, and served it both at Monticello and in Washington. He called all forms of pasta "macaroni," by the way, and usually had it prepared with flat noodles. When at home he used local cheeses made on his and neighboring farms, typically fresh rather than aged ones.