"The Truth is Out There" - The X-Files

"Oh boy!" - Sam Beckett, Quantum Leap

"Highly Illogical" and variations - Mr. Spock, Star Trek

"Dammit Jim, I'm a doctor, not a...." - Dr. McCoy, Star Trek

NCIS' gag about Gibbs with coffee, boats, sleeping :)

Plenty more, I'm sure, but those come to mind immediately

LIP READER!!!!!! *grabs pitchfork* :D

Brain: "Pinky, are you pondering what I am pondering?"

And then Pinky replies with something like:
"I think so, Brain, but if you replace the P with an O, my name would be Oinky, wouldn't it?"
"I think so, Brain... but do I really need two tongues?"
"I think so, Brain, but this time, you put the trousers on the chimp."
"I think so, Brain, but how are we going to make pencils that taste like bacon? Or maybe we should make bacon that tastes like pencils. "