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When flying over another country's airspace, the laws of that country apply. Alcohol, for example, can be banned on certain flights due to international recognition of a foreign power's rights.
That said, spy satellites, Voyager, and the International Space Station don't seem to fall under these rules. This seems to imply an upper limit.
So the question is, how high would an aircraft need to fly in order not to be subject to these rules?
Satellites, the (discontinued) shuttle project and ISS are governed by space law, national airspace laws don't necessarily apply, or are supplemented / amended by international / billateral agreements, on a case by case basis.
That said, the vertical extent of national airspace is a matter of debate. A logical upper limit is the point where outer space begins, as outer space is not subject to national laws. However the boundary is also a matter of debate:
Nevertheless, commercial flights rarely exceed 50,000 feet (15,5 Km), and most have a flight ceiling of 40,000 feet or less (the Concorde was the notable exception). Given that flights over 60,000 feet (ICAO's class A upper limit) typically require special permission, we can safely assume that commercial flights are within national space at all times when flying over a country.
In the near future, with the advent of space tourism the vertical extent of national airspace will need to be more thoroughly defined. Virgin Galactic's SpaceShipTwo, which seems to be the project closer to completion, is not planned to horizontally exceed national airspace. However there are rumors that its successor will be a point to point vehicle, and may complete flights between different countries.
