I've looked around several Fan Fiction websites and YouTube, and found numerous crossovers with FiM involved. Most of the ones I've seen are Sonic the Hedgehog x MLP, and they usually involve Sonic and Rainbow Dash racing.
I once scoured around DeviantART and discovered a Yu-Gi-Oh x MLP Crossover that's still incomplete, but an OK read.
With Team Fortress 2 x MLP, in Fan Fic form, the RED team usually discovers ponies, but sometimes it's the BLU Team.
I would name more, but I think you'll find them.
What Crossovers with Ponies have you encountered?