Yes, it does make a difference, whether you're applying for your first job or running for president. From the New Yorker's James Surowiecki:
American business has a habit of rewarding and punishing people because of the way they look. Since the mid-nineties, Daniel Hamermesh, an economist at U.T.-Austin, has done a series of studies on the role that appearance plays in the workplace, and his conclusion is captured by the title of his recent book, "Beauty Pays." In the U.S., he finds, better-looking men earn four per cent more than average-looking men of similar education and experience, and uglier men earn thirteen per cent less. At today's average wage rates, that means that a man with above-average looks can expect to earn $230,000 more over his career than his ill-favored peers. (The numbers are similar, if less dramatic, for women.)
One study shows that, when it comes to determining income, the important factor is really how tall people were at age sixteen, presumably because people who are more physically mature in high school find it easier to build social capital, make friends, and be leaders. Sometimes, too, businesses that pay handsome people more may be responding to market incentives: Hamermesh cites some evidence (though he says it is "sparse") that better-looking people bring in more business because customers like dealing with them better. That may be obvious in the case of something like sales, but Dutch advertising firms with better-looking executives also had better revenue than their similarly placed competitors.