Usually if I'm saying "beautiful", it's mostly relating to physical appearance, most often the face and particularly relating to her eyes. I have this thing about eyes; don't ask me why, I don't know.
If I'm talking about her personality only, it's usually words like "sweet" or "friendly" or something like that. If I'm calling a girl "amazing", "my dream girl" or "my next ex(-girlfriend)", then it's definitely the whole package that I'm attracted to.
That's not to say that physical beauty can override any personality. If she's incredibly stuck-up or b*tchy, I just won't be able to see her as beautiful, no matter how visually pretty she is.
I believe myself that this is a combination deal. A woman can be remarkably physically attractive, yet I would find her unrelentingly boring and dull if her personality did not suit mine. As well though, I can get along with a less attractive female to a remarkable extent, and not be physically attracted to her in any manner, but it would more than likely end up as a friendship type deal. Overall, there has to be a set standard (which is unique for every individual) on multiple facets of a person for one to truly and honestly tell them they are beautiful and mean it with such sincerity.
Unless you give the line "you're beautiful on the inside"... that always sounds worse than what it is meant to, and I did not realize this until I told this to a friend of mine.