"Du bist speziell."
After reading this, I said this to my (German-born & raised) girlfriend, and she laughed: she said that it is slightly insulting, like saying "you are weird/odd".
She said "du bist besonders" or "du bist einzigartig" would convey a similar meaning to the English "you are special".
If you're thinking of whispering this as a bit of niceness to your loved one: think again!
Here in Spain we can use the word "especial" in both ways. I guess the context is important.
I agree, my dad and fam speak German as a native tongue and say the same thing to give me a hard time ;)