Not only have I pony-fied about half the cast of Half-Life 2, I've also blended the universes. Yes. The crossover reflex has been activated and I must say, the results are actually pretty awesome (in my opinion).
So let's start with this statement: Anything not a human is not getting changed into a pony (with the exception of G-Man and the possible exception of the Vortigaunts, if I can draw a Vortigaunt pony that doesn't look terrible then maybe I'll add them to my crossover world. Sorry folks, that means no DOG pony- he's already a robot creature, what does he need to be a pony for?)
Next let's move on to the world; pretty much the same old Half-Life universe, except with ponies! The Portal Storms, 7-Hour War and Combine takeover are all the same (except with ponies). The whole Combine/City 17 "culture" is a little different, and probably just as dark when you get to the roots of it. (I want to draw a Half-Life E comic, but I'll probably never get around to it so I'll blurt out all my ideas here, sound good? )
The vast majority of the citizen ponies are plain old normal ponies. The Combine systematically eliminated pegasus ponies and unicorn ponies to weaken the overall population; without citizen ponies capable of flight or magic, any resistance would be more easily crushed by forces with the edge of numbers and technology.
In addition, any citizen pony bearing a cutie mark must keep it covered in public. Since a cutie mark is the representation of a pony's individuality, being forced to hide it dulls the individual, making them just another face in the crowd and keeping morale low among the opressed citizens. Most younger ponies who grew up under the rule of the Combine don't even have marks, despite being adults; the restrictions put on them keep them from discovering their true talents.
So that explains a little about the ponies I've drawn. Alyx Prance has no cutie mark, but keeps herself covered anyways to hide her blank flanks. She is also a pegasus pony, but to avoid the attention of the Combine she keeps her wings hidden under her jacket. Isaac Equeiner spends almost all of his time indoors, so he has nothing to fear from being a unicorn and showing his mark.
Anything I missed or left unanswered? Comment and I'll write some more!