So I've been reading HPMOR recently. Ultimately, I was directed there by the Optimalverse group, although it was some time ago that I saw the story mentioned and I've only just now actually read it. I'm currently on chapter 102, the most-current chapter as of this post, uploaded this past July. The author is, among other things, a co-founder of the Machine Intelligence Research Institute, and has blogged about one of the stories in the Optimalverse. So, there's your pony connection.*
The story is, at times, quite hilarious. It's basically a "for want of a nail" story: instead of marrying Vernon Dursley, Harry's aunt Petunia marries a university professor (organic chemistry, if I recall). This leads to Harry being actually adopted by his aunt and uncle, and leading a happy childhood (with no siblings). Additionally, his father encourages him to read all kinds of books that would normally be way above his reading level, resulting in an extremely intelligent Harry James Potter-Evans-Verres, who additionally follows the philosophy of rationalism. There's a very touching scene when Harry's leaving for Platform 9.75 where his father asks if he's bought Harry enough books. It wasn't enough, but it was a good try. (The Verres family motto.)
The story really starts to diverge with Harry befriending Draco Malfoy and snubbing Ron Weasley. Harry and Hermione get sorted into Ravenclaw. Harry begins trying to turn Draco into a Good Guy™ by teaching him SCIENCE! Professor Quirrel is the strongest Defense Against the Dark Arts teacher the school has had in decades, and is one of the only people able to talk with Harry on his intellectual level. Quirrel sets up an extracurricular activity for his students, staging mock battles with three armies per year; Draco, Harry, and Hermione act as the generals of the first-year armies, named Dragon, Chaos, and Sunshine respectively. (And yes, Harry's Chaos army does frequently quote Warhammer 40k. Blood for the blood god! Skulls for the skull throne!)
The intrigue in HPMOR is much more in-depth than in the original novels. Frankly, I'm not even certain that Voldemort is actually still alive in this setting, although some of the characters are convinced that it is so.
Harry masters the Patronus Charm beyond the level at which the adult wizards believed possible, after discovering the underlying Truth about the Charm and Dementors. With this knowledge, he is even able to repel Dementors without any magic at all, and at one point he frightens a Dementor away.
"I make you this one offer," said the Boy-Who-Lived. "I never learn that you've been interfering with me or any of mine. And you never find out why the unkillable soul-eating monster is scared of me. Now sit down and shut up."
It doesn't particularly help when the boy yells "BOO!" at a Dementor and the decaying corpse presses itself flat against the opposite wall and its horrible ear-hurting voice rasps, "Make him go away."
I would also mention that as of chapter 102, Harry is still in his first year at Hogwarts.
It's an excellent read, and I strongly recommend it. It's not short, though! Currently 102 chapters, and author's notes at the end of 102 says that he's written well into chapter 116 already. The notes claim that the schedule puts completion of the story at early 2015.
* Okay, as an additional link to pony, there's the unicorns Quirrel uses to sustain his life. Here's the descriptions given for three unicorns that have appeared:
The unicorn was not white, but pale blue, or appearing so beneath the moon and night sky. Her slender legs stuck out at odd angles, obviously broken, and her mane spread across the dark leaves, green-black but with a sheen like pearls. On her flank was a small white shape like a starburst, a center surrounded by eight straight rays.
Another unicorn lay on the ground, surrounded by a slowly widening pool of silver blood, the edge of the blood creeping across the ground like spilled mercury. Her coat was purple, like the color of the night sky, her horn exactly the same twilight color as her skin, her visible flank marked by a pink star-blotch surrounded by white patches.
He had searched the Grove of Unicorns until he saw her, a proud creature with a pure white coat and violet hair, with three blue blotches on her flank.