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1.
The story behind "What's the frequency, Kenneth?" is actually quite fascinating. You see, William Tager was the local psycho in New York. He thought CBSNews was beaming signals into his head. Naturally, when he saw Dan Rathers walking down the street, he ran up and beat the crap out of him, repeatedly requesting the frequency of the signals so he can stop them, while addressing Rathers as "Kenneth" for no apparent reason to this date.

After this freak event, Tager later shot a CBSNews stagehand. He was then arrested, and told his therapist all the beans.

R.E.M. made a song called "What's the frequency, Kenneth?" The phrase became a nationwide phenomenon. Whenever a cat fell off a roof and killed an old lady, they'd shout it. Whenever they didn't understand a homework question, they'd shout it. And if by any chance, that one son Tager had had with that old lady makes it past the age of five and notices that CBSNews is undetectedly taking over the world through brain control, he may see that one creepy guy who replaced Dan Rathers walking down the street while having a nice stroll down New York and beat the crap out of him, saying "KENNETH, WHAT IS THE FREQUENCY!?"
Teacher: "When A and X are both positive integers in the equation a(4/4)=x and Y is a negative integer in the equation xy=a2, what is the value of Y? Billy?"

Billy: "HOLY CRAP! WHAT'S THE FREQUENCY, KENNETH!!?"
by Spam Spathers March 12, 2005
 
2.
A phrase that was used by a random insane guy that he repeated over and over again as he beat up Dan Rather. Now it's basically used as an exclamation whenever something insane happens and people over-react to it.
"HOLY SHIT! MY CAT JUST FELL OFF MY ROOF AND KILLED MY GRANDMA!"-Guy 1
"HOLY SHIT"-Guy 2
"OMG! WTF! WHAT'S THE FREQUENCY KENNETH!"-Nihilist
by Morpheus August 03, 2004