DARKSEID; “You dare to defy your master Saiyen?!”  
GOKU; “I’ll do more than defy you Sunshine!”

WONDER WOMAN; “What kind of warrior princess are you?!”  
SAILOR MOON; “The kind who isn’t a violent bitch like you!”  

 
SAILOR MOON; “I could really use Tuxedo Mask’s help right about now.”  
WONDER WOMAN; “No man can bail you out of this!”

ALUCARD; “You should be afraid human!”  
BATMAN; “I’ve met circus clowns scarier than you!”

ALUCARD; “Only a human can destroy me demon!”  
SPAWN; “I’m dragging you to hell regardless!”

ALUCARD; “You are not worthy to be my No-Life Queen!”  
MARCELINE; “You’re not my type old geezer!”

Nightmare Moon: The night shall last forever!  
Werelight Shine: Oh yeah? Well, I’ll make you wish it was daytime when I’m through with you!

Celestia: You will not harm my subjects!
 
Luffy: MEAT!

Rarity: Oh, Spike, you are so brave!  
Spike: Try not to hate me for this!
 
Applebloom: I toldja, I’m a big pony!  
Applejack: You’re still my baby sister.

Discord: Insert horse pun here.  
Celestia: What’s the matter? Run out of material?
 
Sombra: This world belongs to the Darkness.  
Pinkie/Discord: Uglysayswhat?
 
Random Cute charecter: I’m Cuter!  
Random Cute charecter: NO! I’M Cuter!
 
Maybe instead of hitting you, the really cute characters just stop short, and then do something which is heart renderingly adorable.

Dan: PINKIE PIIIIIIIIIIIIE!  
Pinkie: Yeees?~

Equestria Girls Twilight: This is a good way to test out this form.  
Pony Twilight: Here’s the catch, it’s gonna hurt!
 
or
 
Pony Twilight: Despite the new form, you still fight the same as me.  
Equestria Girls Twilight: Let’s see if anything is new then!

Some ideas with some of my and my friends’ original characters;
 
Fencer: Let’s test who’s gotten stronger!  
Shining: Fine with me, Shining!
 
All-Star: Let’s get this party started!  
Applejack: Ain’t gonna be a cakewalk for ya, sugahcube.
 
Cosmo: I do say, this is most unusual.  
Cosmo: I concur.
 
Justice/Karn: You could never understand my pain!  
Shining: Don’t you patronize me!
 
Fencer: I hope you won’t be mad at me, Twilight.  
Twilight: I couldn’t be.

Apple Bloom: “Ya think we’ll get get out cutie marks for this?”
 
Scootaloo: “Only one way to find out.”
 
 
False Cadance: “All I want is your love.”
 
Shining Armor: “Where’s my real wife?”
 
 
Rainbow Dash: “Come at me with everything you got squirt.”
 
Scootaloo: “You got it Dash.”
 
 
Cadance: “You wont take there wills ever again”
 
King Sombra: “I will have what is rightfully mine!”
 
 
Non-Cannon (fanfics,comics,blogs ect.)
 
Scootaloo: “I thought you loved me?”
 
Rainbow Dash: “How could I ever love a failure like you.”
 
 
Love struck Derpy: “Change Him back!”
 
Discord: “I have no idea who your talking about my dear.”
 
 
Celestia: “How can you do this?”
 
Solar Tyrant(AUTCB Celestia): “Humans are incapable of harmony. How couldn’t I?”

Garble: You little pipsqueak!  
Spike: This pipsqueak bites back!
 
Shining: I gotcha, Cadance!  
Cadance: Don’t sell me short, Shiny.

cheerilee: “shnooky-lumps!”
 
Big Mac: “schnoodle-bump!”

Mr.Cake: are the kids asleep?
 
Mrs.Cake: Don’t worry, we’re good for now.

Lyra: “You think I’ll just HAND you a victory?”  
Bon Bon: “Ugh. Enough with the puns already!”

Rainbow Dash: I’m the fastest in all of Equestria!
 
Trixie: Oh good, I like a moving target.

@Background Pony  
That one is pretty clever.

Orion: Twilight’s heart is mine Comet!
 
Comet Tail: In your dreams Orion!

Pinkie: Come with me if you want to live!  
Future Twilight: That’s not funny.

Faved this for the comments, I love most of the clash lines in Injustice.

Twixie:  
Twilight: Don’t bet on your luck Trixie!  
Trixie: The Great and Powerful Trixie doesn’t need luck!
 
Rainbow Dust:  
Rainbow Dash: Who’s the wingpony now?  
Lightning Dust: I’ll send you back to flight school!

Twilight: Don’t take it easy on me, BBFFF!  
Shining: Wouldn’t dream of it, Twily!
 
Chrysalis: I will consume your love!  
Cadance: My love is too much for you to handle.

“So, Applejackstar, Celestiagurt has taught you well… And I see your Schwartz is as big as mine. Let’s see if she taught you how to …handle it.”