1. Get up
When it's safe to do so and when you feel the need, get out of your seat and walk around the cabin. This will give your legs and hip flexors a good stretch and get the blood pumping. It's easiest to go for a meander on long-haul flights with wide-body aircraft. Try to do this every 45 minutes to an hour on longer flights.
This one is easier to do when most people are sleeping or seated and cabin crew have finished meal service. Find an unoccupied corner, possibly near the lavatories, and practice squatting down (like your sitting in a chair that's not there) and standing back up. This will work the back and front of the legs as well as the booty. 15-20 times will be sufficient, but if you feel good enough to do more, go for it.
3. Upper chest stretch:
Here's one to do if you've scored an aisle seat. Stand up facing the window and reach up as high as possible on the overhead compartment, keeping your head below the bin. Once your arms are as high as possible, drop your head in between your arms and hold that stretch for about 15 seconds. This will stretch the upper torso muscles that are usually tight from carrying luggage and being seated.
For those of you lucky enough to be flying on a Boeing 747 or an Airbus A380, find that set of stairs and put them to good use, but only if it doesn't block cabin crew. Put one foot on a step and lift you body as if you are ascending the staircase. Return to set while keeping that foot on the step. Perform this about 15 times and make sure you repeat on the other leg.
If you're flying on an airline that offers a self-service walk-up snack bar (like at the back of Economy on a Qantas A380, or Business' new bar in the middle of American's 777-300ER), when the coast is clear and the rest of the passengers are fixated on their movies, head on over to the counter top. Place your hands on the edge about shoulder width apart and bend your elbows and lower your chest to the ledge. Then push back up. The only thing that might make this exercise worthless is if you then grab a few bags of chips to head back to your seat.
As a word of caution, if you're planning to perform any of these mile-high movements make sure you're not interrupting the crew or imposing on the personal space of others. And it's best to talk to you doctor first since some huffy puffy at elevation is definitely different then on terra firma.