Befriend the flight attendants
When we asked flight attendants what they hate most about their jobs, their biggest complaint was rude, irrationally angry passengers. Realize that flight attendants are not airline management, and are usually in no way to blame for delays (they only get paid when the plane is in the air), and maybe, ya know, try being nice to them instead. Don't be too eager and annoying, because that'll just make them hate you and erroneously blame you for farts in your area, but if you're cool when you're waiting for the bathroom and you ask them interesting questions and show you’re funny and have good taste in Kelme sneakers, you can get all sorts of hookups. Also, they can tell you how to have sex on the plane.
Never use the bathroom during beverage service
It only takes one time walking out of the bathroom, seeing the beverage cart 20 rows in front of you blocking the way to your seat, and being forced to make small talk with someone whose face is 8 inches from your crotch, to learn to never do this again. Either jump up as soon as the 10,000-foot bell goes off, or wait until after the beverage service is done.
If you have to poop, remember this
It's actually better to go when there's a small line, rather than no line, to avoid detection as the pooper. Treat it like a bar bathroom in terms of expediency and courtesy flushes. And this is the most crucial: act like you, too, are grossed out by whomever pooped BEFORE you when you come out of the bathroom. Maintain eye contact with the next person. Losing eye contact will prove that you are ashamed and thus were the pooper.
Also take this pearl of wisdom from Neil Patrick Harris' flying and packing tips to help cover your tracks: "You laugh, but this is effective -- use hand soap. Put it on your hands and all over your arms, and do, like, tai chi moves with your arms. Then wash your hands, and then the bathroom doesn't smell like your stuff. Every time I do it I'm impressed with myself."
Get up and stretch every 90 minutes or so
I read somewhere that your legs atrophy and you get blood clots and possibly die if you don't. I REALLY READ THAT SOMEWHERE.