Military-grade sensors, telecommunications equipment (the current aircraft have 87 telephones and 19 televisions each), additional exit points, a completely remade interior, including the President's private quarters, a kitchen, storage equipment, cold storage equipment to store enough food to serve hundreds of people (or a few dozen people for several days, there was an article about a $20M fridge a few years back), anti-nuclear shielding, reinforced glass, separate quarters for guests, senior staff, Secret Service and security personnel, a medical annex, which includes a fold-out operating table, emergency medical supplies, and a well-stocked pharmacy, the president's executive suite, a conference room, modified engines.
Air Force One does not have a fighter escort most of the time.