Friendship, the Final Frontier.
When a Starfleet ship discovers that the Orion Syndicate is enslaving ponies, her commander decides to do a good deed and return the rainbow-maned pegasus home to Equestria. Things don't go smoothly for the crew of the USS Judges, but what they find may be one of their biggest discoveries ever.
A Friendship Is Magic/Star Trek Online crossover.

In an effort to keep her mind occupied, Twilight Sparkle decides to delve once again into the grand mysteries of Pinkie Pie. This time, Twilight's focus is on her claims of growing up on a rock farm: like so many things related to Pinkie Pie, the idea that somepony could grow rocks as an agricultural product makes absolutely no sense. However, the investigation eventually leads Twilight to a rather... surprising discovery.

This is the first story in The Petriculture Cycle.

Artwork by Page Turner. Now with a TV Tropes page.

Only fools, madmen, and adventuring parties go into the Malpheggi, the swamp beyond the Everfree Forest. It can be left as an exercise for the reader as to which of these categories Samus Marcus (a Thyatian swordsman, or so he says) and Ivan (his companion in trouble) fall into. When they are rescued by the registered adventuring party, the Elements of Harmony, a grand quest across the D&D world of Mystara begins. Together they face culture shock, international politics, romance, dungeons, and a dragon with a grudge as Marcus learns how to trust his new friends and make up for his past mistakes while the Elements of Harmony try to save Equestria from a threat which proves more... complicated... than they originally thought. Also, pie. And hats. A D&D (Mystara)/MLP Crossover.