I know that there are some RPGs focused on ponies, such as Ponies and Parasprites, and other RPGs have official support for ponies (My Little Legend being a good example)

What games do you know of that include ponies?

Let's see:

Don't Rest Your Hooves

Fallout: Equestria

Laser Ponies

My Little Pony: Roleplaying is Magic

Ponies & Parasprites

Pony Tales

Pony Tales: Aspirations of Harmony

The Savage World of My Little Pony

Unknown Ponies

I've recently started looking into running Unknown Armies with my regular group thanks to discovering Unknown Ponies: Failure is Awesome. I can't really run Unknown Ponies with my group, because one of the guys just isn't interested in MLP -- he's watched a couple episodes, but decided against it.

Unknown Ponies: Failure is Awesome really intrigues me, though. I especially like how the friendship track works, simultaneously as XP, manipulating the actions of NPPs (non-player ponies ), and a reward for both roleplay and out-of-game actions. "Learning from your mistakes," by getting +1 in a skill when you fail a skill roll, is also entirely in-theme with the setting. Just reading the rules of the game, I can agree with Erin (creator) that it works better to play as foals than as adults.
Unknown Ponies: Failure is Awesome (blog post contains link to most up-to-date version of the rules, v2.5 as I write this)
Kelpies (rules for playing kelpies as a race, rather than just earth/pegasus/unicorn)
Renaming/Cute-ceañera
Zebra alchemy rules
Character sheet
(You should also find a copy of the Unknown Armies core rules, because there are some things in there not in Unknown Ponies that you'll still want to use.)

Here's another one, the My Little Pony FemtoRPG, mentioned in IRC.

939135
There's also the now official Tails of Equestria game. Look it up if you don't know what it is.