I can't really vouch for a "legitimate" use in that I believe it truly is a violation of a persons rights ( I am refering to questions regarding personal issues, likes , dislikes, sexual practices/history, beliefs etc, things that are private and hurt no one, and are definitely no one else's business) I would like to see some of the senators on the Hill that support Polygraphs have to answer these questions.
However from a law enforcement perspective I can definitely tell you that the Poly and CVSA are excellent interrogation tools and that is the key word "interrogation" because it is the confessions you get before the test that are what make it work, yes it is a real useful tool for investigators that other wise wouldn't be able to solve a crime without a confession. The test itself is nothing but a fraud and calling it a science is an insult to all other sciences.

Augster,

One conceivable legitimate use for polygraph technology is the Guilty Knowledge Test (GKT) developed by Dr. David T. Lykken. It is theoretically much sounder than the Control Question Test (CQT), which is the standby technique of the American polygraph community (and that to which dimas and Gino referred). You'll find the GKT briefly described at p. 63 of the 1st edition of The Lie Behind the Lie Detector and more fully in Lykken's book, A Tremor in the Blood: Uses and Abuses of the Lie Detector.

The GKT is rarely used in the United States, however, as the CQT is easier to administer. In addition, the GKT is not amenable to screening applications.

The GKT, like the CQT, is vulnerable to countermeasures.