What's that smell?
Believe me, sometimes you just don't want to know. Anytime you cram a bunch of people in a long, metal tube and close the door on them, somethings going to smell. . . bad.
What can you do about it? Usually, nothing. But if it's beyond the normally offensive smells, you should contact your Flight Attendant while you're still on the ground. There may be options.
. . . it’s a relief to know that at least some airlines are actually willing to do something about evil aromas. In their conditions of carriage , American declares you can be booted from a flight if you “have an offensive odor not caused by a disability or illness.” The right of determination is granted to the flight crew, but you must raise the issue early (i.e. before takeoff) in order to have the best chance of a favorable resolution.
In an article in the L.A. Times, a more detailed list of options and remedies are explained, including removal of the offending passenger(s), upgrades, changing seats, and re-booking on another flight. It's delicately handled.
Speaking up may not solve the problem, but keeping quiet definitely will not.