"Hare Rama" is a mantra, associated with the Hare Krishna Movement, a Hindu cult/religion founded in 1966.
Rama himself is an ancient Hindu king, worshipped as a deity by Hindus. (http://en.wikipedia.org/wiki/Rama)
Zappa mentions "Hare Rama" twice, in Can't Afford No Shoes, where he sings: "Hey everybody/Nothing we can buy/Chump Hare Rama/Ain't no good to try." and in The Meek Shall Inherit Nothing, where he states: "Is Hare Rama really wrong? If you wander around with a napkin on/With a bell on a stick an' your hair is all gone /The geek shall inherit nothin' "