LOL. I don't know I'd call that iconic, per se, but it certainly was the most frequently heard line from that series.

Not from a game, but from a movie.

"Don't just stare at it, eat it." - American Psycho

"You should have known better."

HoMM III

"You almost became a Jill-o sandwich".

For some reason this one has stuck with me:

"Come in Chosen one..."

and a couple more from my favorite RTS:

"I said a bow string, not a g- *sigh* nevermind..."
"Godess, light my path"
"Ready to work"
"This... is.... my... BOOOMSTICKK!!"

Dawn of War had a couple of golden ones (which I hope I remember correctly):

"The emperor rules all alien. You'll learn that soon enough."
"Blessed is the mind too small for doubt."
"Secure the advantage!"
edit: couple more from this impossibly kickass game:
"An open mind is like a fortress with its gates unbarred and unguarded"
"He who stands with me shall be my brother"

Feeling... lonely? -7th guest

Stay awhile and listen! -Diablo

What was that? Must have been rats. -Any NPC in elder scrolls IV/V as they walk over their now dead comrade.

"Stay a while and listen."

Ninja'd, lol.

"All your base are belong to us" - Zero Wing

"Look at you, hacker: a pathetic creature of meat and bone, panting and sweating as you run through my corridors. How can you challenge a perfect, immortal machine?" - System Shock

"But thou must." - Lady Lora, Dragon Quest

"Matsuba!" - the alien companion, Another World

"Jill, here's a lockpick. It might be handy if you, the master of unlocking, take it with you." - Barry Burton, Resident Evil

"Yup, that's a cow alright." - hero, Diablo