Spiders and Magic: Rise of Spider-Mane (also read here) is a Spider-Man/My Little Pony: Friendship Is Magic crossover fanfic by Maximus_Reborn. Trouble is brewing, and Spider-Man is summoned to save the day! However, he takes the form of a pony upon his arrival and slowly starts to lose his powers. Now as Peter Pony Parker, he must become Equestria's new hero as the Amazing Spider-Mane, but with past failures haunting his mind, will somepony be able to give him the happiness he deserves and save him from a prophecy that ends with his death?Across Equestria and through Earth, two hearts will join together, but one may die to ensure the other's survival...Still ongoing, as of 2014.
Alternate Continuity: The Spider-Man of this fanfic seems to have elements from both, the mainstream Marvel universe, and the Ultimate universe, as well as some elements from the films (The final consensus seems to be that he's the "Amazing" Spider-Man from Shattered Dimensions, though Edge of Time doesn't seem to have happened yet). It is also an alternate continuation of MLP Season 3, since it takes place after Sombra's first defeat in the Crystal Empire.
And an offhand comment in chapter 53, reveals that even Marvel vs. Capcom has already taken place in this continuity.
Turns out, this story's Marvel Universe is numbered 672, though it's apparently a close neighbor to 616.
To elaborate, he has his main relationship with Twilight, but every single one of the Mane 6 (except Pinkie Pie) are attracted to him, and Sweetie Belle and Scootaloo even have precocious crushes on him. And that's just from the main cast. Princess Luna finds a lot of common ground with him, Trixe treasures his friendship as her first friend, Derpy fangirls over him and even Spitfire likes him.
Darker and Edgier: Obviously, when compared with MLP:FIM, especially since it incorporates some elements from the Ultimate Marvel universe (which loves this trope). For the most part, however, it's a pretty light story.
Defrosting Ice Queen: There is a non-romantic example, with Peter trying to win Princess Luna's trust, and even teaching her to loosen up a little in the process. The non-romantic part starts to get a little iffy after he succeeds, especially in chapter 35.
The Determinator: Spider-Man, obviously. When the ponies start to learn more about his past and his reputation back in New York, they can't help but admire his willingness to keep fighting for people that distrust him or outright hate him.
Also, Rainbow Dash, when trying to prove that she's a better hero than Pete, and going as far as to enter into a dragon's lair as a "Test of Bravery".
And Lyra, and her obsession with proving that Spider-Mane is a human.
Heel Realization: J. Jonah Jameson has an extended one during the four year period after Spider-Man's 'death', taken to the next level when Osborn's broadcasting of the final battle reveals Spider-Man's identity - a kid who suffered Jameson's abuse his whole career, even accepting a pittance of a salary for defaming his own alter-ego, yet kept fighting the good fight.
I'm Having Soul Pains: From the battle in the Helicarrier, to the battle with Sunset Shimmer, the ponies who have developed a close relationship with Peter, start feeling pain whenever he's close to die.
Leotard of Power: Part of Twilight's costume after her trip to Earth with Peter and Spike.
Le Parkour: Since the buildings in Ponyville tend to be only two stories high, this is Spider-Mane's main form to move around.
Let's Get Dangerous: While Equestria citizens admire Spider-Mane, they won't become aware of his full power until his seemingly hopeless duel with the Princesses of the moon and the sun. Hopeless, indeed.
Not So Stoic: Trixie, and much to her embarrassment, most of the time.
Luna is feeling the effects of this, as well.
Not What It Looks Like: In chapter 12 when Rarity and Applejack find Peter pinned to the ground in the royal garden, and hugged tightly by Fluttershy. Turns out that she was only frightened by Princess Luna's appearance.
Prophecy Twist: The prophecy states that Peter will die at the hands of a closely trusted ally. The prophecy says nothing about that ally being consciously in control of her own actions, nor does it state that the ally can't use magic to bring him back to life.
Second Love: Twilight, especially since Word of God states that she serves as the Mary-Jane of this story (except that Twilight is more capable of defending herself). Funnily enough, Applejack, who has had the least Ship Tease with Spidey (aside from Pinkie Pie), reminds him of Gwen.
Shout-Out: Peter does this quite a few times, much to the confusion (and in Twilight's case, annoyance) of Equestria's denizens, since they can't get any of the references. True to his usual style, he continues LONG after Twilight voices her displeasure... or because of it.
Chapter 42, when Peter tries to think of a superhero name for Twilight, he suggests... Equestria Girl.
Chapter 43 ends with the intro Marvel Ultimate Alliance without Spider-Man.
Peter's second and final battle with Sombra (spanning chapters 50 & 51) is almost beat-for-beat the same battle Samurai Jack has with the cursed Viking warrior.
Also, Princess Luna and Rainbow Dash to a lesser extent.
Weak, but Skilled: The cast's assessment of Spidey when he's going against Spitfire. Spitfire is naturally faster, but Peter has his Spider Sense and the acrobatic agility to go full speed at all times while she has to slow down. At all OTHER times though, this does not take.