Scorpion: You canot escape death  
Rainbow Dash: I can sure as hay try  

Tirek: You think you can topple me!?  
King Sombra: You delude yourself to think otherwise.

Scorpion: You’ll brun in hell!  
Tirek: I’ve Survived Tartarus
 
Shang Tsung: Your soul is mine!  
Celestia: Immortals can’t have their souls taken!  
(i know kinda lame ^)  
Ermac: We are Many You are but One!  
Luna: And we will destroy you!
 
Spike: I’ll burn you  
Sub-Zero Ice Doesn’t burn

@Background Pony #BC66  
I can do better.
 
Tirek: I shall defeat you with magic!  
Superman: … and a lot of wishing!
 
(I know I stole this from an actual clash quote from the game, but that won’t stop me!)

@ThisGuyHasNoName  
Ok then:
 
Tirek: EQUESTRIA SHALL BE MINE!  
Megatron: Fool! There can be only one conquerer of worlds!

I wonder if we’re ever gonna bring Tirek into this….

@masterhand01  
Lobo: Don’t mess with the Main Man!  
Rainbow Dash: And don’t you mess with the Main Mare.
 
Rainbow Dash: Eat my dust, loser!  
Lobo: I’ll eat the rest of ya, too.
 
Lobo: This is my kinda party!  
Pinkie Pie: It’s a bit dull. Just like you!
 
Pinkie Pie: If you give up, I’ll give you a free cake!  
Lobo: I’ll make you into cake.

@masterhand01  
Ooohh, nice burn AJ!

Lobo: How about a pony-skin cap?  
Rarity: That’s last season, darling.
 
Rarity: I’m surprised you aren’t naked, you barbarian!  
Lobo: I’d be happy to fix that, chicky.
 
Lobo: Gonna string you up with that pink mess!  
Fluttershy: I-I’d really prefer you didn’t.
 
Fluttershy: Ummm, d-dolphins.  
Lobo (suddenly calmer): What about dolphins?
 
Lobo: You’re gonna get fragged, bastitch.  
Twilight Sparkle: Those words are NOT in the dictionary.
 
Twilight Sparkle: You have a lot to learn about friendship.  
Lobo: I’m an expert at decapitation though.
 
Applejack: You prefer a hoofprint on yer face er yer keister?  
Lobo: I’d prefer some fingerprints on your ribcage.
 
Lobo: That cider’s weak as piss!  
Applejack: Funny. So are you.

Robocop: You are no longer under arrest.
 
Joker: Where’s my Get Out of Jail card?  

Thought of a few more quotes, this time from TF2:
 
Heavy Weapons Guy: NOW IS COWARD KILLING TIME!!!  
Snowflake: YEAAAAAAAAHHHHHHHHHH!!!
 
Spy: Sorry to pop in unannounced!  
Rarity: Perhaps you should ring the door next time!
 
Pyro: Mmph mpmh!  
Pinkie: I agree, this will be fun!
 
Scout: Too slow!  
Rainbow: I’ll show you who’s too slow!
 
Solider: You have dishonored this entire unit!  
Derpy: I just don’t know what went wrong!
 
Sniper: Wave goodbye to your head wanker!  
Twilight: I’ll keep my head thank you!
 
Demoman: If I wasn’t the man I was I kiss ya!  
Zecora: You are drunk and unwise, this I despise!
 
Engineer: I’M GONNA LAY YOU OUT!  
Applejack: Not if ah’ do it first!
 
Medic: Prepare for your examination! Evil Chuckle  
Fluttershy: I’M GOING TO HURT YOU…that is if you want it…

Sombra: I won’t lose to cupid’s cannibalistic, little sister.  
Chrysalis: You’re going down you socially-inept Mary Sue.

Cheese Sandwich: Smile!
 
Maud: I am smiling.

Discord: Do you know what you’re dealing with?  
Commander Shepard: Don’t underestimate us mortals.  

Evil Celestia: I saved my Equestria!  
Canon Celestia: By being a tyrant!?
 
Nightmare Rarity: You know in your heart you are weak-willed.  
Rarity: Trust me, I’m not alone!

@Marshal805
 
I Love that response.

Dumbbell: Your mom kept me up last night!
 
Button Mash: That’s impossible! She only likes stallions!

Discord: Rainbow Dash ALWAYS dresses in style!  
Rainbow Dash: OH SHUT UP!
 
Seabreeze: Good things come in small packages!  
Queen Chrysalis: Then it’s a good thing I’m evil!
 
Twilight Sparkle: Your going to pay for your enslavement!  
King Sombra: For me, it was Tuesday…
 
Nightmare Moon: You can’t defeat your true self!  
Princess Luna: Good thing you’re not…
 
Spike: Had enough, Bird-Brain?  
Gilda: Watch it, Lizard-Boy!
 
Blueblood: So you’re in love with that hussy, Rarity.  
Spike: I’m gonna enjoy pounding your skull in…
 
Unicorn Twilight: It’s like, looking in a mirror.  
Alicorn Twilight: Only, not.

Expert Tracker: Here Piggy, Piggy.
 
Expert Sniper: Oink, Oink.

Trixie: You’re cute when you’re angry.
 
Sweetie Belle: Then I’m about be adorable!

Raindbow Dash: Let’s go, booze hound!
 
Berry Punch: Try not cry, light weight!
 

 
Rainbow Dash: This is for hogging all that cider!
 
Berry Punch: You really need to let that go, kid.
 

 
Luna: You’ve finally learned to show a lady a good time.
 
Blueblood: Very funny, Auntie.
 

 
Fluttershy/Rarity: I’ve had it with your attitude!
 
Bon Bon:
 
(To Rarity): What was your name, again, Drama Queen?
 
(To Fluttershy): Looks like somepony got herself a backbone!
 

 
Rumble: Remember, this isn’t game!
 
Button Mash: I still plan to win!
 

 
“Cupecakes” Pinkie: Looks like I need to make a freah batch.
 
Pinkie Pie/Lyra/Discord/The Doctor: And everypony says I’m a crazy!
 

 
Carrot Top: Stay out of my fridge!
 
Derpy: Stopy making such tastey food!

Blueblood: “How dare you strike me!”  
Gilda: “I didn’t need to be dared!”
 
Future!Twilight: “How’s that tummy ache, Spike?”  
Spike: “Better than your battle scars!”
 
Spike: “A proper gentleman should respect women.”  
Blueblood: “A proper gentleman shouldn’t let them use them!”
 
Gilda: “Just like old times.”  
Rainbow Dash: “Keep being nostalgic, it makes you easier to hit.”
 
Cheese Sandwich: “Last time I was in a fighting game, I was the ref!”  
Pinkie Pie: “Hey, that’s MY shtick!”
 
Blueblood: “I don’t see why Auntie had such trouble putting you away!”  
Discord: “I don’t see why she isn’t doing the same to you.” (Also works with NMM and Sombra)
 
Chrysalis: “Come now Shining, this was supposed to be perfect.”  
Shining Armor: “It will be once I get my flyswatter…”
 
Celestia: “This is why Rarity left you…”  
Blueblood: “Because of my fighting skills?”
 
Blueblood: “Beating up a little girl is beneath me…”  
Diamond Tiara: “Being beaten by one clearly isn’t.”
 
Gilda: “Stupid smoke and mirrors!”  
Trixie: “The Great and Powerful Trixie WISHES she could afford that!”
 
Discord: “Is tea still on next week?”  
Fluttershy: “Of course…”
 
Spike: “Give back Twilight!”  
Sombra: “All the princesses are mine now.”
 
Discord: “Maybe you should lighten up.”  
Sombra: “Try to be my jester AFTER I’m king.”
 
Sombra: “Stop with your childish insults, you fool!”  
Diamond Tiara: “I bet your horn got bent on the way down the ugly tree!”

@masterhand01
 
Fou-Lu: We didst not know Endless could be equine.  
Celestia: That’s not all I’m going to teach you.
 
Celestia: Are you sure you’re not a magical princess?  
Fou-Lu: Knave! We are the First Emperor!
 
Fou-Lu: We were also split into two halves. Thou haveth our sympathy.  
Luna: We never requested it!
 
Luna: We wish we could’ve slept those thousand years!  
Fou-Lu: Wouldst thou like to sleep for eternity?
 
Fou-Lu: Your love of Humans is misplaced.  
Lyra: Says you!
 
Lyra: Just tell me about the Humans!  
Fou-Lu: Thou could not handle what we have to say.
 
Princess Twilight: I didn’t think the human world was so bad.  
Fou-Lu: Then thou hast been misled.
 
Fou-Lu: Thou hast escaped the Human world as well, have you not?  
Princess Twilight: You make it sound like a prison!
 
…what can I say? He’s easy to write for.

Black Adam: You dare strike Khandaq royalty?  
Luna: We do.
 
Green Lantern: Beware my power.  
Sombra: Beware mine!

Surprise: Your fans aren’t gonna like what I’ll do to you!  
Pinkie Pie: Oh please, I kicked your flank to get on the show. Remember?.
 
Discord: You’re a has-been, my little, nearly-extinct birdy. What makes you think you can even compare to me?  
Gogo the Last Dodo:(LoonyToons) You made it rain chocolate milk. You haven’t seen what the sky does, when I’M around!
 
Amaterasu: …  
Celestia/Luna: Twilight? There’s someone here to “see” you!
 
Yeah, okay I can’t really think of a serious one for those two.