I just got back from a flight to Spain at 32 weeks. The most important thing you can do is drink tons of water before and during the flight (I drank about 1/2 liter every half hour - not club soda or anything else with too much sodium). That way you're forced to get up and walk around (to the bathroom) every 30 minutes or so. The water can also help prevent and sometimes even stop early contractions (according to the flight attendant).
I avoided airplane fare and just brought fruit, nuts and cheese (to avoid sodium, etc.) If you can't get the extra leg-room or an upgrade, make sure you request an aisle. And wear comfy shoes that are about one size too big, just in case of swelling.
I also wore support stockings (maternity hose, not knee-highs), just to be on the safe side. If you can, bring an extra pillow/pregnancy pillow with you, so you can semi-sleep on your side. Also, make sure you are carrying virtually no carry-on (the added weight will add to discomfort) and take an extra day once you arrive to sleep/stretch, hydrate and relax.
I had a great time and would do it again, but every body is different - you just have to listen carefully to yours...