In my opinion this is caused by 3 things: the time difference, lack of sleep and dehydration. For this reason I always drink a full bottle of gin before getting on a plane - that way you won't even know you're dehydrated. Vodka should work too if you can stomach the rancid stuff.
It's important to keep your circulation going while on a longhaul flight. A little bit of exercise is ideal for this. I recommend fucking the flight attendants. You'll find they're often willing (especially the female ones). Also you need to make sure you have plenty of legroom. Best thing to do, when noone's looking, is to whack whoever's sitting either side of you over the head (the empty gin bottle comes in very handy for this - make sure it's one of those chunky glass ones), and quickly stuff them into the overhead locker. They should be fine up there - and hey, they'd have done it to you first if they only thought of it, right? Then you can lie down and relax for the remainder of the flight.