If you want extra leg room, ask for seats by emergency exits or doors. They have more leg room than regular seats due to FAA regulations. These seats are usually only available at check-in.
If you want privacy from your in-flight neighbor, put on a set of Walkman headphones -- even if you are not listening to them. Be sure to bring a comfortable set of headphones if it's going to be a long flight.
Drink an adequate amount of water. Due to the regulated pressure and temperature of the cabin, the body tends to get dehydrated very fast; this contributes to jet lag. It's a good idea to keep drinking water throughout the flight.
Minimize alcohol and caffeine intake. Alcohol dehydrates the body, as does caffeine. If you do have a drink containing alcohol or caffeine, be sure to counter it with an extra glass of water.
Keep stretching and moving around. By moving around, you can prevent the blood from pooling in your lower extremities, thus minimizing fatigue and jet lag. People with any kind of heart problem should definitely attempt to keep moving, as this reduces heart strain from lack of blood.
Dress comfortably. Your body swells slightly due to fluid accumulation on long flights. Tight rings, shoes, and waistbands can cause considerable discomfort. Loose fitting pants and shirts and elasticized waists can make life much more comfortable.
Dress in layers, or carry a light sweater or covering with you. Airline cabins tend to have large fluctuations in temperature. If you do not wish to carry an extra piece of clothing, request a blanket from the cabin crew when boarding.
Carry a change of clothes with you. In case of any unfortunate spills, you will be able to change your clothes immediately.
Eat a light meal. On a long flight, it is easier for your body to digest a light meal than a heavier, more complex one.
If you have special dietary needs--vegetarian or kosher, for example--be sure to cofirm at check-in that your meal will be available. This is especially important if your plans changed at the last minute or you have been bumped to another flight. And, since mistakes happen, bring a snack with you just in case, as insurance against going hungry.
Remember to put the "Do not Disturb" sign on your seat rest if you intend to sleep. This will prevent you from being disturbed for that extra drink or cup of coffee. It is also a good idea to fasten the seat belt on the outside of your blanket where it is easily visible to prevent the flight attendant from waking you up to check if it is fastened.
Be nice to the flight attendants. They have a hard job and are taking care of a lot of passengers, and have the power to make your trip significantly more--or less--comfortable. Asking for their assistance in a calm, pleasant tone is much more likely to get you what you want.
Jet Lag
As a general rule, it takes a day for your body to adjust to each time zone crossed. Jet lag is often more common and more dramatic in your eastbound travel (e.g., from Tokyo to San Francisco than from San Francisco to Tokyo).
If at all possible after transcontinental or transoceanic flights, don't plan on conducting important business the day you arrive. Instead, use the day to get your circadian rhythms back in sync.
Avoiding alcohol, regulating your diet, and being sure to get plenty of sleep and exposure to sunlight are effective methods to deal with jet lag.
When Ears Get Plugged
If you are suffering from nasal congestion, take a decongestant or nasal spray before your flight. For a long flight, take it again about an hour before landing.
If you feel excess pressure in your ears, open your Eustachian tube by yawning or swallowing. You can also chew gum or ice.
If you are traveling with children, make sure they're not congested yourself--they probably won't think to tell you. Also, as soon as the descent begins, pass out the chewing gum. Don't wait to be asked: that won't happen until they're already uncomfortable, if at all. Save nursing infants' meal, or part of it, until the descent; nursing will help keep their ears clear.