There are a large number of Pokemon Creepypastas out there, but I believe Lost Silver is one of the first (its the first one I read, anyway). It's not really even that scary, but it's pretty sad in a way. It won't make much sense to you unless you're familiar with the franchise. I used this one to represent all the great gaming Creepypastas out there.
You start out in the sprout tower, and every time you enter a new area your team changes. You almost always have a full team of Unown, a Pokemon that is shaped like a letter of the alphabet. They will spell out things like "LEAVE" or "HEDIED", etc. Anytime you check your trainer card, your character appears more mutilated, losing all limbs, blood streaming from his eyes, and eventually turning ghostly white. You have almost no interaction with anybody else; the NPCs ignore you, and when you battle Red at the end the fight makes no sense, as you battle each other with impossible movesets. At the end, you find yourself in a grave, and the words " I'm dead." show up on the screen. There is an alternative ending that occurs about halfway through when the character chooses a different answer when they are asked if they want to continue.
Again, probably the least spooky pasta on my list. I think it's just the idea of taking a beloved part of my past (I am a huge fan of the series) and twisting it up. There are videos to go along with the story, and you can play the hack yourself.