I like the Youngsters battle line in Pokemon.

"I like shorts! they are comfy and very easy to wear!

Call of Duty: Ghosts: Extinction

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   "Intel reports the last extinction squad to come through this town went MIA!"

   "Ugh, look at this place. It's been a bloody battleground since they were unearthed."

   "Spectre One, take this drill and destroy any hives on your way to the crater! Arm that nuke and haul ass back here! Let's go. Good luck, gentlemen!"

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Link to Quotation: http://www.youtube.com/watch?v=Z7pyEx_1TbA (Watch the first forty seconds of the video.)

Oh and i like Pokemon Stadiums narrators voice when a battle ends. "And there goes the battle!" It always makes me feel gifted, but if i lose, It just cheers me up and then i try again.
And i never played the portal games, But i watch walkthroughs. And my favorite is when Glados says "I am a potato."

The only one I can think of now is: "The ones who steal are the ones who win in this world." - Lysandre, Pokemon X and Pokemon Y . Lol. Probably not my TOP favorite, though.

Definitely
"Nothing is true, everything is permitted"
I still have no idea what it means yet in my mind it remains one of the coolest things ever said.

another good one would probably have to be from Kingdom Hearts

Ansem: You see darkness is the hearts true essence
Sora: You're wrong! The heart may be weak it may even give in. But deep down theres a light that never goes out
Ansem: You've come so far and still you understand nothing

and lastly from Saints Row one of the secret agents
"If I die, tell my wife I have another wife"

I died upon hearing that

"Phooey! Emperor Gesthal's stupid orders! Edgar, you pinhead! Why do you
have to live in the middle of a stinking desert?!? These recon jobs are
the pits! ...AHEM! There's SAND on my boots!"

"Son of a Submariner! You'll pay for this!"

- Kefka Palazzo from the Final Fantasy VI

Beginning of Sonic The Hedgehog 2, when they say "SEGA!" In all that 16 bit glory.

All your base are belong to us.

Pure happiness in one poorly translated sentence.

Duke Nukem:
"Time to kick butt and chew bubblegum- and I'm all outta gum!"
"Power armor is for p******!"
Skyrim:
"I used to be an adventurer like you, until I took an arrow to the knee."
GTA V:
"F***in' A"

I think my all time favorite game line came at the end of Kingdom Hearts 358/2 days.

After playing the entire game as Roxas, it ends with him being put into this coma-like status, and having this virtual world projected around him. His last line in the game is "Maybe today we'll finally hit the beach!"

And it's just this really huge moment because you realize that you've been playing a prequel this whole time, and that all your actions lead up to the beginning of Kingdom Hearts II, and I swear I get teary-eyed every time I hear that music come on afterwards.

Such a great moment.

Here are some of my favorite lines 
Mega man X4: Zero: WHAT AM I FIGHTING FOOOOR?
Mega man X7: Axl: When we kicked that big dude's Butt I though 'YA!' We'll make a PERFECT Combo!
Mega man Legends 2: Tron: *cough Cough* Well there There goes another Gu- *cough cough* Gustaff *cough cough* but it doesn't matter WE'VE WON! Bons on his way up to the surface *cough cough* What why's your face red? WHY IS EVERYONE LOOKING AT ME THAT WAY? Servbot1: Umm Miss Tron, your clothes have been umm kind RIPPED OF! Servbot2: actually your clothes are um GONE! Tron: What huh? *screams like she is surprised* Y-YOU GUYS! WHY DIDN'T YOU TELL ME BEFORE! RETREAT RETREAT! Both servbots: R-Roger!
thats all i can think of

NalaTheLion : "Do a barrel roll!" made me laugh. lol Also, my favorite SM64 quote would be when Mario sleep-talks "Nightlight...Ah Spaghetti...ah Ravioli...Ah Mama Mia". It may also be that he said Night Night, but I always thought it was Nightlight. Anyway, I would let him fall asleep just to hear him say it. lol

My personal favorites (in no certain order):
"We ain't gonna make that gap." "We'll make it" "Ain't gonna." "We'll make it." CRASH! "What did I tell you?" More of a conversation, but hilarious when you see it still. Also from the same game: "You were kicked in the head by a horse, Oui? So the brain does not work right?" "How'd you know about that?". Those were both from Tomb Raider Chronicles, and it's been years since I found them, so I may have missed a word or two.

"La La La" Toejam & Earl.

"Oh man. That's my fighting arm. What a drag..." the ancestor mummy from Tak and the power of JuJu.

"Here, take the staff mighty warrior. You are meant to have it....and don't ever touch me again! Mmmhmmmm" Same as above.

The scene with the Tak quotes (skip ahead to the start of the fifth minute of the video to see it):

Here is few from Final Fantasy VI, I like Kefka because he is so honestly evil, and quite a funny fellow. There is lot of more good lines just don't have time to find them all. So these 3 will do.

My favorite line from a video game is "kept you waiting, huh?" -snake
From metal gear solid

My favorite was Jak 3 death scene when daxter says alright cut were the Director I can't work like this.

I'm a big fan of the Metal Gear series, and i've quoted Snake already in real life. It was weird, but it was awesome at the same time.

One of my favorite lines is(This is not the entire line, but it's the important part): "A name means nothing on the battlefield. After a week, no one has a name." That's from Metal Gear Solid 3: Snake Eater, during the Virtuous Mission.

My favorite line is from Portal 2. When Wheatly replaces GLaDOS, he says something in Spanish. End's up that he actually said "You are using the translation module incorrectley, please reffer to the instruction manual for proper usage".

My favorite line is from Mario Party and Mario Party 2. I just love it when Wario keeps saying "D'OH I MISSED" I don't know why but I just really think that is very freaking hilarious.

Hmmm, I don't remember any good lines in video games, but recently I in youtube I found a meaningless line from a game that you might never heard: HOTEL MARIO! And I find it amusing to me.

Mario : "You know what they say: All toasters toast toast!"

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