According to you, what is the best story on this list?

That's a tricky one... Depending on my mood, my top three choices might be Homunculus, Yuureitou, and Ultra Heaven (or really anything on the first few pages). I can't say any of them are the best, but they're all awesome in their own right. If you've got something specific in mind, like if you're looking for something really gory or really sad or really trippy at the moment, I could recommend something more specific