Frequent (and infrequent) flyers will want to review the excellent Air travel health tips at AirHealth.org. You’ll find information about warning signs during air travel that can indicate serious health conditions as well as general tips on keeping healthy during long flights.
A few general tips are to exercise during your long flights using “isometric” exercise where you pit one muscle against another, pushing your hands together for example. Another approach is to “walk” in place, pushing down on the floor with one foot after another. You’ll also want to take a few walks up and downthe isle during your flight, perhaps adding a few ‘laps’ during trips to the restroom.
Also be sure to keep hydrated – it’s easy to dry out during the flight, so make sure you drink at least as much as offered by the flight attendants. Note that you can always have a beverage *and* a glass of ice water – just ask politely.
Sleeping on the plane is another important health issue, especially on very long flights. I find that neck pillows and earplugs are a great sleep aid. Dramamine or an antihistamine like Sudafed will also help if you have trouble sleeping.