Ah, yes, the classic armrest scenario. The fact is that the way plane seats are configured, someone is going to get one armrest, while someone else gets two. If you find your seatmate's elbow is poking well into your space, I've found a couple of "inadvertent" bumps with your own elbow or a book usually does the trick.
If the person really seems intent on resting both arms, you've got a decision to make: Do you really need that armrest, or are you fighting just on principle? If it's the latter, the simple, direct approach is really your only bet. Anything more aggressive will make you look like a schmuck.
Keep in mind, this scenario is likely to occur when someone is stuck in the middle seat — that guy already has a bad enough situation, so why not let him enjoy some leisurely arm relaxation?
Then there's the ongoing issue that passengers have had to deal with since the invention of reclining seats: the seat back against your knees. Unfortunately, that's the way seats recline, and it's a ripple effect that starts with the person in front and continues to the poor guy who's stuck in a nonreclining seat all the way in back.
This is really a case-by-case situation. Be aware of your surroundings. If the person in front of you is 6-foot-3 and obviously struggling for space, take one for the team. But it is OK to speak up if it's in the middle of meal service, and the person in front of you suddenly slams his or her seat back while you have food and/or drinks on your tray. That's actually a dangerous situation.
A good rule of thumb is to keep your seat upright or partially reclined until after meal service and then go ahead and sit back. (Now we just have to get the rest of the plane to follow this rule.)