Pliskin: You don't get injured in VR, do you? Every year, a few soldiers die in field exercises.
Raiden: There's pain sensation in VR, and even a sense of reality and urgency. The only difference is that it isn't actually happening.
Pliskin: That's the way they want you to think, to remove you from the fear that goes with battle situations. War as a video game — what better way to raise the ultimate soldier?
Raiden: So you're saying VR training is some kind of mind control?

— Metal Gear Solid 2: Sons of Liberty. Pretty haunting quote about the dangers of videogames...in a videogame. --

"Ahh,, do you not feel the grand romance of the wide open skies? The roaring invitation of the wind? The soft call of the clouds? You are a boring, boring creature."
  --Willi, the Bird-Man in Wind Waker

"Let's make like Eggman's hairline and receded!" - Sonic in Sonic Colors
!!!
Can you tell I loocooooove that line?

@Retro_on_theGo O_O I was going to say that.... oh well.

NO COPYRIGHT LAW IN THE UNIVERSE CAN STOP ME! - Sonic Colors.

Hah, it's an awesome line. Of course someone else would want to put it.
I also love the line you put! XD

The Suicide Note from Resident Evil: Revelations. I love that game.
"It's the end of the line for me. I have only one bullet left. Lot of good that'll do me in a fight. Nope, that bullet's all for me. So long, everybody. It was a good ride while it lasted."

Hey you! Get offa my cloud!

"I don't like boys!
I like little girl-... no wait, that sounds wrong too!" Ragna the Bloodege, BlazBlue Continuum Shift II.

"People deal with grief differently - some **** at funerals - I cut of heads." - No More Heroes 2

I have loads more from those games. Love them.

SUPER SMASH BROTHERS MELEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

"It's so cold."

• Sharla, Xenoblade

Pretty much anything Riki says especially this:

Riki: "Aww... Riki wish Melly real sister-pon"
Melia: "Aww... What about Sharla?"
Riki: "Sharla more like mama-pon. Riki think one Mama enough"
Sharla: "Now just hold on one minute!"

"Doh I missed". - Wario from Mario Party

Goggles: "How Are the Amaze-O-Gaze Glasses working out? I'm sure daddy cane fix them if they're broken,"
Kazooie: "But can anyone fix daddy?"
Goggles: "W-why does he need fixing??"
Banjo: "Er... Kazooie means your mom is just fixing up his dinner,"
Goggles: "Oh, that's alright then. I was afraid you ment he'd been blasted by a fatal spell or something!"
Banjo: "Ulp!"

Don't know about 'Favorite' but here's a couple from KIU:

"Souls are like bacon" -Hades

"Go home Hades....just go home..." -Pit

And the dialog about Melee and Brawl when you are using a bow.

Does anyone know if a non-video game quotes topic ha already been created?

I just love it when Hades says: 'When freaky alien give you lemons, make freaky alien lemonade!'

Please... Pit clearly has the best lines, not Hades...

"And I'll take you for a walk! And maybe even give you a treat! We're gonna rack up some serious Nintendogs Trainer Points together!" <- Best line of anything ever.
"I AM NOT DOING A COMB-OVER!"
"Should have practiced more in Light Versus Dark..."
"Step Three: Remove Pants!"
"Haaades...!"

There's nothing like the thrill of a good solution!

-Hershel Layton

"Time to kick ass and chew bubble gum and I'm all out of gum"

Duke Nukem.