I view "special" as meaning something that is not statistically frequent. I don't consider it to be good or bad. In reality, I doubt the definition I use is common because it seems to either compliment someone or belittle them, perhaps even simaltaneously. Alternatively, it is used to compliment someone on being themselves, although I don't quite understand whether this usage is meant to be positive or negative since it tends to be over-used so much.