A few years ago I have had the experience of being a flight attendant for El-Al Israeli Airlines.
It was a great experience that had taught me much about life and the human (and especially Israeli) nature, and one of the most important things I had learnt was how to manage your flight as a passenger and make it as convenient as you can.
Following are some tips I believe can make a more comfortable flight:

1. Head start - Make sure to be one of the first passengers to check into the flight, this way you can have better seats to chose from.
   
2. Choosing a seat - I think that unless you are suffering from prostate problems the window seats are the best you can get.
   The front rows of the airplane have much less turbulence than the rear ones.
   
3. Carry on Luggage - Make your carry on luggage as small as you can, but be sure to pack one set of underwear, a couple of books, a pen (for those landing forms) and a toothbrush.
   
4. Toilet - the best times to visit the toilet is right after take-off, and between meals.
   
5. Drinking - Drink as much water as you can.
   It will make you use the toilets more often and make more walks as well as prevent you from dehydrating.
   
6. Alcohol -Although some airlines serve free alcohol, it is not recommended to drink any alcohol during the flight since the airplane air is thin and dry, if you add some alcohol to that you're on your way to dehydration if not blood poisoning.
   Trust me, I've seen in happen.
   
7. Sleeping pills - If you decide to take some sleeping pills during the flight, take a low dosage - sleeping pills have a much stronger effect on you when you're up 20,000 feet in the air.
   From my experience passengers who have taken a larger dosage just kept on sleeping after the flight had finished.
   
8. Travel pillows - a good travel pillow will help you through your flight.
   The best travel pillows are the bigger and thicker ones, the simple travel pillows you are better off without.
   
9. Your relationship with the flight crew - Be nice to the flight crew, respect them and politely ask for whatever it is you want.
   Do not command the flight attendants or demand things off them, or you will get to their bad side.
   Flight attendants (like any other person) cooperate better when you talk to their hearts and make them empathize with you.
   
10. After landing - do not stand up until the "fasten seatbelt" sign has been turned off.
    Passengers who do stand up end up being crammed by other passengers who didi the same with no ability to get back to their seats for as long as the airplane hauling takes, and that may take up to 15-30 minutes!

Enjoy your flight!