Many flight tracking websites have the data about almost all the commercial airplanes in air. Do they have the data about the private jets and/or defense aircraft also and they just don't show that on the websites?
As long as an aircraft transmits (unencrypted) ADS-B information, anyone within radio range can track it. The equipment necessary to receive ADS-B can be as simple as a computer with a TV receiver (USB DVB-T module) and the right software.
Receivers can then send the data stream to, for example, Flightradar24, who will display it on their website.
As Flightradar24 states, not all aircraft are equipped with an ADS-B transponder, and even those that do may not have switched it on. Unless ADS-B is installed and operating, it would not be visible.
@ezra-g mentiones that Steve Jobs' aircraft was blocked, but this is of something one would have to ask for, and the site has to apply the filter so it doesn't display on its website. However, Jobs' plane would still have been visible on the receiving computers. And, of course, the website will only filter your aircraft if they are willing to do so, either on request, through payment, or a government order.
Flightradar.com also has some other data sources, like FAA (Federal Aviation Administration) radar information in the US, which also contains aircraft without a transponder. The FAA may also filter some aircraft.
From the FlightAware FAQ:
How does FlightAware handle flights around the world? What is FlightAware's service area?
FlightAware's primary service area includes airspace operated by the United States (including Alaska, Hawaii, Puerto RIco, and Guam), Canada, the Caribbean, Australia, the United Kingdom, and France. Flights in the primary service area support real time maps, departure and arrival information, delays, and more.
FlightAware's secondary service covers scheduled major airline operations at any airport in the world. Flights in the secondary service area support departure and arrival information. Secondary coverage areas may have real-time positions for ADS-B equipped aircraft operating in FlightAware's ADS-B coverage area. Additionally, some airlines send FlightAware satellite position reports from aircraft worldwide that augments other position data and provides transoceanic coverage as well.
For flights arriving in a service area from outside of a service area, FlightAware will be able to track the flight when it nears a service area. For flights departing a service area, FlightAware will be able to track the flight until it leaves the coverage area. Flights may not be tracked beyond that point unless they enter another service area.
Not all worldwide data sources (e.g., European data, datalink ARINC/SITA ACARS, etc) are freely available on FlightAware.com due to government regulations or commercial arrangements. You can contact us if you have a commercial need for worldwide data.
Flight tracking websites, such as FlightRadar24 and FlightAware, generally track aircraft using publicly available ADS-B transponder information. Privately operated aircraft are included as long as the owner of the aircraft has not specifically requested that their aircraft be excluded from public searching. For example: Steve Jobs' private plane's N-number was public information, but it was excluded from tracking on Flightaware.
Military aircraft are not included in public ADS-B tracking information.
Yes, recently PlaneFlightTracker provided exactly this live service both for NATO and Russian Military aircraft as well as Medical, Emergency, Safe and Rescue helicopters and airplanes. It starts with a procedure explaning how to track as well as Live Military Aircraft Maps. This site uses the FlightRadar24 map for embedment but has made an effort to extract necessary ICAO codes so that the users may get the proper maps.