I liked both of them pretty much equally. Creepy Black was obviously more fictional and less possible than the other, as the main point of the story was something that wouldn't be possible in the old games unless you took the time to add the coding to make it possible, which honestly I don't think anyone would go through with if it was only with one single copy, however the story was quite creepy and I was a bit freaked out, though I usually am with most stories.
Lost Silver was a bit more believable though, as everything that wasn't normally in the game in the story was something that could be added through ROM hacking, as proven by some people who have actually gone through with hacking a ROM to reenact the story in an actual game. Lost Silver was also pretty creepy, though most of what the story entailed was not really anything I could be freaked out by just through words, so it needed some kind of visualisation too.
Either way, both of them were pretty creepy despite both of them being so different, though I think I'd have to go with Creepy Black.
