My favorite would be:
"Go for the eyes, Boo!" said by Minsc in Baldur's Gate. That line still pops into my head during certain situations even a decade later.
Also, some of Imoen's lines pop into my head for entirely different reasons. I'll not even repeat the lines lest they get stuck in someone else's head.

Every single one from Duke Nukem 3D.
Also: "War, War never changes" from Fallout.

Fool me once, shame on you; fool me twice, watch it! I'm huge!
There is strength in numbers, and I am two or three, at least.
Butt kicking for goodness!
Boo points, I punch - it's a very simple relationship, but it is effective!
Go for the eyes Boo, GO FOR THE EYES!! RrraaaAAGHGHH!!!
You point, I punch.
Less talk, more fight!
When the going gets tough, someone hold my rodent!
Make way evil! I'm armed to the teeth and packing a hamster!
Magic is impressive, but now Minsc leads! Swords for everyone!
I need aid soon, lest my hamster become an orphan.
Boo likes the forest.
We are all heroes; you and Boo and I. Hamsters and rangers everywhere, rejoice!
These bars will not hold my wrath. Minsc will be free! Butts shall be liberally kicked in good measure.
after question how mincs get his monster in BG2 - Boo is small and evasive, and there is ever so much of Minsc to search.
Boo must have his exercise, lest he bite us all in hard to reach places.
Ahhh, I prefer the bright day; evil must be able to see the justice I dispense!
Then say it louder! We must inspire fear in evil! Quiet tales of hamsters are foolish, but a man and his hamster that tear evil limb from limb? That's scary!
*Squeak* Boo says that he was just doing his job.
Every hamster has his day!
Jump on my sword while you can, evil! I won't be as gentle!
this one is best ingame, not written - Oh... Oooh... ooh, you are a smart one! I understand now! You said what you did just to make me mad, mad enough to break free, ha ha! You are as smart as Boo sometimes!
even rangers with head injury need magical weapons - No effect?! I need a bigger sword!
even hamsters have bad mood - He mutters occasionally about fellow hamsters that will kill you all, but he is just moody, so don't worry. See how he glares? Shhh, we should leave him be.
battle hamsters - What? Boo is outraged! See his fury! It's small, so look close. Trust me, it's there.
and last one :)
Minsc: Then say it louder! We must inspire fear in evil! Quiet tales of hamsters are foolish, but a man and his hamster that tear evil limb from limb? That's scary!
Protagonist: Ahh, what the hell. Right-o, Minsc! Our deeds will ring in the evil ears we box and label do not open 'til mid-winter fest!
Minsc: Now you are speaking the language of Minsc! Next we must get you a hamster! Or perhaps an ice weasel, whatever your tastes.
there is never enought of minsc
and quiz for end : My brother's a +12 Hackmaster!
who was this ? :)

There are so many classics from Tachyon: The Fringe...
"Whooa, that's a [pause] big gun!"

Yeta/Blizzetta from The Legend of Zelda: Twilight Princess.
"Pretty... Pretty... mirror... Lovely... NOT TAKE MIRROR!"
i think this is the best and most unexpectable thing that would happen right before boss fight.

moon that was an epic post! i laughed so hard
high rate!

Dangit... I could look it up, but I'll just be honest about it. It was the sword that you got by doing some riddle in a sewer. It was actually a pretty nice sword, but a tad annoying. My paladin actually used it before getting the Avenger. Man, I almost have it too! I know exactly where it is... under the Temple District! Grr...
Also.. thanks for all the Minsc quotes, I had forgotten half of them. And yeah, I think the in game one where you annoy him to bend the bars of his cage is one of the best as well.
Edit: I found the name through google. I never would have remembered it. I'll let someone else take the glory of naming the thing. Blah, I remember the room you get it in so clearly. There were 4 things you had to put in order. One was blood, as i remember, but I can't remember the other 3. Pretty simple riddle actually.

"Uh"
Fallout 2 character with INT 1

There's a veritable shitload of brilliant quotes from Giants: Citizen Kabuto
TIMMY: Righto! Mine's Achmed, but you can call me Timmy.
BAZ: Bloody hell! Look at the size of this thing! Come on lads, we've gotta try this one out!
BORJOYZEE: Dammit! I've got the raft, but I'm gonna need help. You lads mind helping me rescue Timmy? For I'm just an old man, plus me balls are saggy.
BORJOYZEE: (After taking a leak against a palm tree) Yeah! And there's more where that came from!
TEL: Good Lord! I thought Timmy was ugly!
TIMMY: Pills! I need my pills mister Baz! I'm very high strung, you see, and-and-i-and-i and I need my pills!
ROBOT: (In a stilted robot voice) Hel-lo Meccs. (In a normal, albeit panicky voice) F*ck me! The reapers are coming! The reapers are coming, I'm outta here!
YAN: Yan always speak like this when on mission!
YAN: Ah, blue lady speak with tongue of butter knives.
YAN: The evil queen Zapho? Isn't your mother Sandra Myrtle from Chilchuck Island? Oh, well then forget what I just said about me being your father.
YAN: Yes indeed. She says you must now all run into oncoming traffic with your genitalia exposed. Wait, Yan is wrong. She says you must protect this base while she is away building up her strength.

"What can change the nature of a man?"

for your answer there is first price :) all minsc quotes (or at least most of them) -
http://en.wikiquote.org/wiki/Baldur%27s_Gate_series
http://www.minscandboo.com/quotes.php

Gunther Hermann and Anna Navarre in Deus Ex:
"Are you sure you pressed the right button?"
"I do not make mistakes of that kind!"
"Your hand might have slipped."
"No, I pressed orange. It gave me lemon-lime."
"The machine would not make a mistake."
"It's the maintenance man. He knows I like orange."
"So you think the staff have some kind of plot?"
"Yes, they do it on purpose!"
Shogo: Mobile Armor Division:
Sanjuro:
"Ah, the most embarrassing moment of my life, and no one to share it with."
"Anything else I can do for you, you crazy old bag? Take out your garbage maybe?"
"Yes sir! You are my personal hero sir!"
"I'm going to rip Ryo's leg off, and kick his ass with it!"
Sanjuro and Kura:
"What are you doing?"
"I ran into some stragglers who were trying to eat a cat."
"Can you repeat that, slowly?"
"Pervert."
"I'm having trouble picturing it. Maybe you could demonstrate."
"'Maybe?' You must have amnesia!"
UCA Trooper:
"I have my orders sir, PLEASE BE NICE TO ME!"
Caleb, Blood 2:
"Hmm... 'Point away from face and fire.' Sounds easy enough."

YOU INFIDEL BURN IN HELL, this quote is from fallout 1