Empty seats in the economy class is not the airlines’ problem. Actually airlines suffer because of this phenomena, which squarely reflects economic softening. Nothing that the airlines can do about.
Empty seats in the Business and First Class is serious matter though. It beats me how airlines allow that to happen and not upgrade folks that are cramped in coach class. It is such a powerful gesture that is guaranteed to delight a customer. At the gate say “Sir, this is your new boarding pass. We upgraded you to Business. Complimentary. We hope you have a comfortable flight with us” if the airlines could sort out the bumless-seats upfront. If there still are empty seats, locate the person most uncomfortable in the lower class (someone single in a middle seat, someone right at the last row where the seats don’t incline completely) and make her day by guiding her to the higher class of comfort. When the marginal cost of upgrade is zero (okay, not completely zero but very close) then upgrade as many as possible. Make the switch experience dramatic for the user by skipping an intevening class if you can (take row 56E straight up the staircase to First Class). The simple gesture of costless upgrading buys a lifetime of loyalty for the airline. The airlines don’t get it.
The same thing applies to Product Marketing. If your product ladder has Base, Gold and Platinum versions then give away the lowest marginal cost difference items to some of your most irate customers.