Metal Gear has fallen into the hooves of an Equestrian revolutionary, who, with the backing of his human mercenary allies, intends to use it to depose Celestia and crown himself ruler. Having crossed into Equestria in pursuit of this rogue weapon, the legendary Solid Snake must ally with the residents of Ponyville to prevent a nuclear catastrophe.

See also Equestria Gear Solid, the hilarious spin-off EQG parody in which everything you know is wrong, and every single character from the story is an awful caricature of themselves.

Now with its own TVtropes page!

Celestia, while surveying her kingdom, is informed of a strange, rather mad bipedal prisoner in macabre dressings and wielding a number of strange possessions...along with a bloodied kitchen knife.

Warning: Silliness inbound.

By order of the high lords of Terra themselves, a lone soldier from the Death Korps of Krieg has been sent to the planet Epona to wipe out its Xeno population. Starting with Equestria, the Korpsman has sworn not to leave the planet until he falls or completes his mission.

However, no Korpsman should fight without setting up a proper trench first, and so the Korpsman must dig...and dig...and dig.

Destroying Equestria is going to take a while.

Instead of being killed in the cold Antarctic by Dr. Manhattan, Rorschach finds himself rematerialized in a strange new, pony filled world. He finds himself drawn into the lives of the ponies of Ponyville but some ponies fear that this sociopath will bring danger and darkness to an otherwise peaceful existence. Will the mane 6 help Walter Kovac find peace within himself or will he bring them all down with him in his cold views of reality and existence?

As Seen on Equestria Daily!
And our TvTropes page (By Crowrob0t): http://tvtropes.org/pmwiki/pmwiki.php/Fanfic/RorschachInEquestria

My Little Pony: Friendship is Magic and its likeness is owned by Hasbro Studios. Rorschach and Watchmen are owned by DC comics. All rights go to their normal original, intended owners.

*REWRITTEN*

Eager to vindicate herself about her steadfast belief in the fabled existence of humans, Lyra turns to a "special interests" firm to acquire a prime specimen of the legendary bipeds. Or two. Or three. Or four. Or a dozen. Or a thousand...

FEAR crossover

The protector, otherwise known as the Big Daddy, is often regarded as the ultimate killing machine of the underwater utopia known as Rapture. They are nearly indestructible, can endure the crushing pressures of the bottom of the ocean, and possess a variety of killing tools.

Through a completely unexpected sequence of events, a Big Daddy is sent to Equestria through a tear. Knowing the kind of havoc a Big Daddy can cause, Booker DeWitt and Elizabeth pursue the behemoth to get it back.

But they're too late.

Takes place in the BioShock: Infinite- Burial at Sea universe, in an alternate timeline. The events of the DLC Burial at Sea: Episode 1 do not happen. Booker and Elizabeth are not trying to find Sally. NONE of your favorite ponies are getting killed, I promise.

A Bioshock Big Daddy wakes from his stasis in Equestria, and subsequently adopts an unwilling Apple Bloom as his little sister. This is the short tale of the events that followed his awakening.

Marko and Ishmir are polar opposites. But that’s what makes the Spartans so good together. So good in fact they can take on a whole Covenant space station and win.

Unfortunately extraction didn’t go too well, and the headhunters find themselves stranded on an unexplored planet. Can Ishmir keep the peace with the locals and get the Spartans home; or will Marko cause an interstellar incident?

My money’s on the latter.

Halo (non-canon) vs. My Little Pony (season 4) Crossover

Rated Teen for gratuitous swearing, violence and suggestive themes.

This story is a sequel to Stardust

When Equestria’s newest member of royalty asks for aid to be offered to her friends from abroad, the best and the brightest volunteer to serve. Captain Steel Song of the Dusk Guard are immediately mobilized to help XCOM defend their world from the enemies that besiege them. However, their first joint operation with the humans takes a turn for the worse and they quickly find themselves fighting for their lives against the full force of the monsters that threaten Earth.

(Stardust/Dusk Guard crossover)
(Coverart provided by a friend of Viking ZX!)
(While familiarity with both stories isn’t required, it is recommended)
(Many thanks to Arzoo for pre-reading!)
(All screenshots can be found at XCOM.wikia.com)
(Featured on 3/13/2013. Thanks everyone!)
(Now has it's own section on TVTropes as part of the Stardust series!)

Anonymous is the Chosen Undead; the so-called hero of Lordran. After the final confrontation with Gwyn, Lord of Cinder, Anonymous is ripped from his world and thrown into Equestria. A stranger in an even stranger land, Anonymous must make due with the fact he's stuck there while searching for a way to return home. But when forces conspire against Equestria and Anonymous, will the so-called hero be able to save both the land and himself?

(My entry into the budding Anonymous in Equestria group, here on FIM.)