A pony can choose to do many things in his or her life before he or she dies: he could be a farmer, bringing in produce and commerce to the kingdom, or she could be a rebel, fighting to further her cause. Death visits everypony, however: the farmer hopes to leave his farm in capable hooves before he passes, and the rebel hopes to have finished the fight for whatever cause she was fighting for before her time comes.

Sometimes, death likes to come calling early: the farmer taken before his prime provides no additional produce; and the rebel becomes a martyr, causing others to fight in her place.

Sometimes, rather than kill a pony, it is better to leave him or her broken.

An accident with one of Twilights latest invention creates a dimensional rift sending, Trixie, Pinkie Pie and Bon Bon from Equestria to Earth, in Present Day Iraq. They find themselves right in the middle of a warzone at the height of the now dubbed second insurgency. The scales of power that are already unsteady threaten to tip completely, as their accidental arrival may threaten to ignite an already tense, global situation and push the world powers and mankind into its most devastating and horrific conflict to date. It is the beginning of the end.

Twilight becomes alicorn of the stars. This is sort of a problem, because Luna kind of already was alicorn of the stars. Oops!

TV Tropes

Worgen? Try Ponies as the new Alliance race instead! Deathwing's Cataclysm breaks open the seals separating Equestria from the rest of Azeroth, allowing in the insanity that is World of Warcraft and WoW players.

I also recently got a spin off! Check it out!
"A Day at the Quest Hub" by Braininthejar
http://www.fimfiction.net/story/77999/a-day-at-the-quest-hub

WoP TV tropes page here:
http://tvtropes.org/pmwiki/pmwiki.php/FanFic/WorldOfPonycraft

It is the year 2552 and the Pillar Of Autumn has just entered Slip space to escape the Covenant fleet at Reach. A malfunction occurs with the Slip space drive and sends the Autumn and her crew into unknown space. The first planet that comes into range is very Earth like, and is giving off intelligent life signatures. What they don't know is that their only way back home is on this planet. The Autumn dispatches a scout party and what they report back is unbelievable. A world completely inhabited by ponies, millions of them..... Welcome to Halo: Equestria.

I'll add in more character tags as they are introduced in the story.

Cover image is: My Little Mjolnirs: Friendship is Mark VI
by *COBilly
Fan Art / Digital Art / Drawings / Games ©2012 *COBilly

Halo is the property of Bungie and Microsoft.

My Little Pony: Friendship Is Magic, is property of Hasbro and Lauren Faust

I do not own the cover image, Halo, or My Little Pony: Friendship Is Magic.

Luna, knowing she still must improve her standings with much of Equestria asks a favor of Celestia:To let her host the next Grand Galloping Gala. Celestia refuses and offers a better idea, To let Luna host her own Individual celebration. Luna soon finds out the troubles of planning such a grand event.

Two years after Nyx was stripped of the Nightmare's power, Twilight Sparkle is attempting to raise Nyx as a normal filly. But as Nyx's magical abilities begin to grow out of her control, the pair quickly earn the attention and ire of some powerful ponies who do not have Nyx's best interests in-mind.

During the night, the Elements of Harmony mysteriously vanish, and Princess Celestia enlists the aid of their bearers to find them. Twilight is forced to choose between her duties to her princess and her duties to her daughter. In the process, she discovers a web of conspiracy surrounding her daughter that reaches back a thousand years into Equestrian history. Will Twilight be prepared to face the things she learns along her journey's path: about Nyx, about Celestia, about Equestria, about the Elements...

...about herself?

Based on Past Sins by Pen Stroke Pony.
Alternate universe, because Twilight never became an alicorn or princess in this story.

After a mishap involving the Transportalponder, the Courier finds himself in a place he doesn't recognize. With no way back and nothing else to do, he decides that wandering into the nearest town is the best option. Being the Courier, things aren't that simple...

A Fallout: New Vegas/My Little Pony: Friendship is Magic crossover

The style alternates between omnipresent third-person and the Courier recounting his tale to... Well, take a guess.

Samurai Jack finds his way to a strange land that holds an ancient secret. There, he and the native ponies must fight together in a battle for the fate of the world.

The Decepticons come to Equestria to obtain all their resources. With the Autobots stuck on Earth, and magic having little effect on Transformers, the Decepticons have little to oppose them. Starscream is pulled out to a different light from seeing the planet and starts to remember how he used to be before the Cybertronian war and little more 'organic' insight of the planet.

Rainbow Dash however isn't going to let her planet go without a fight and she has back up from an unlikely source.