What are you, some kind of bottom feeding, scum sucking algae eater?
Duke Nukem 3d

From Blade Runner:
Clovis - "I thought I could cheat destiny. I should have cherished... what time I had... instead of... wasting it."
Gordo - "What does a marriage and a tornado have in common? First there’s a lot of sucking and blowing and then you lose your house."
Crystal Steele - "I can handle it from here, Slim, why don’t you go buy yourself a lolly pop? Something else to suck on."
Ray McCoy - "You wake up one day and find it’s all been a dream or you wake up and discover you’ve been asleep all the time and the nightmare is real. I didn’t know what it was. I didn’t know what I was. A cop dangling on the short end of a stick or a Replicant who’s memory banks had run out."
And from the beginning of the game:
Runciter - You can’t possibly have anything that would interest me. These are extremely rare models of the highest quality.
Clovis - What a coincidence, so am I.

My favourite quotes are from duke nukem 3d
What are you waiting for? Christmas
Your face, your ass, what's the difference.
I'll rip your head off and shit down your neck!

"You fight like a dairy farmer!"
"How appropriate. You fight like a cow."
"Look behind you, a three-headed monkey!"
The one regarding the beard has already been posted :)
All hail Guybrush!

"Doesn't appear to be working." -Adam Randall, Realms of the Haunting
Not funny, not clever, not anything. But my brother and I have been using it for over ten years. That's impressive longevity.

You, sir, are now one of my close friends; let me embrace you as a brother.
Guybrush: "Did I say cannibal? I meant cannonball; I want to be a cannonball! BOOM!"
*AWKWARD SILENCE*
Lemonhead: "You're not quite stable, are you?"

Choice Baldur's Gate ones...
M (About Sarevok's return) "Eh? He is like a bad penny, this one. An armored, deep-voiced penny of most sinister evil!"
M "What? Boo is outraged! See his fury! It's small, so look close. Trust me, it's there."
L "What's my status? Since when do you care about me unless I'm impaled in something's guts? Oh well, fine, let me think for a minute... Well, as a matter of fact I would like to register a complaint. I want to kill a dragon. Right now. Go find one and kill it. That would be SO cool."
JI "Typical. If I had a sense of humor left I might find that funny. I do not, on both accounts."

Plug time!
A bomb!
(Rate it five stars).

"Where is it!?!?!" from Duke Nukem 3d when you press the space bar too many times trying to find that damn secret door...

I like the one from Shadow Warrior better.
"Oh damn, I'm running into walls now!"

"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?"

Careful there, DanSavi, Fenixp might see you XD

Well he didn't post it so it was my duty :P

Well of course I didn't, this quote can't be used lightly

GLaDOS has the best lines:
While safety is one of many Enrichment Center goals, the Aperture Science High Energy Pellet, seen to the left of the chamber, can and has caused permanent disabilities such as vaporization.
Audible warning devices are required on all mobile equipment. However, alarms and flashing hazard lights have been found to agitate the high energy pellet and have therefore been disabled for your safety.
The Enrichment Center is committed to the well being of all participants.
Cake and grief counseling will be available at the conclusion of the test.
Did you know you can donate one or all of your vital organs to the Aperture Science self esteem fund for girls? It's true!
The Enrichment Center reminds you that the Weighted Companion Cube will never threaten to stab you and, in fact, cannot speak.
Although the euthanizing process is remarkably painful, eight out of ten Aperture Science engineers believe that the Companion Cube is most likely incapable of feeling much pain.
Place the device on the ground then lie on your stomach with your arms at your sides.
A party associate will arrive shortly to collect you for your party.
Assume the party escort submission position or you will miss the party.
Remember when the platform was sliding into the fire pit and I said 'Goodbye' and you were like 'no way' and then I was all 'I was just pretending to murder you'? That was great!
There was even going to be a party for you. A big party that all your friends were invited to.
"I invited your best friend the companion cube. Of course, he couldn't come because you murdered him.
All your other friends couldn't come either because you don't have any other friends. Because of how unlikable you are.
It says so right here in your personnel file: Unlikable. Liked by no one. A bitter, unlikable loner who's passing shall not be mourned.
'Shall not be mourned.' That's exactly what it says. Very formal. Very official.
It also says you were adopted. So that's funny, too.