어디예요 Where is it?
어디 있어요? Where does it exist? Where is it located? (sounds a bit more specific)
This is what I think the difference is. I think I say the first more often - if I always say the second instead, I'd sound demanding.
I'll be watching this question to see what other Koreans think about it.
----------------------------------------------------------------------------
Let me add some more. For stuff, we say "어디 있어요?", not "어디예요?"
그 책 어디 있어요? Where is the book?
그 책 어디예요 doesn't make sense.
그 식당 어디예요? Where is the restaurant?
그 식당 어디 있어요? Where is the restaurant located?
지금 어디예요? Where are you now?
지금 어디 있어요? Where are you now? (sounds a bit specific, it's asking the listener's location)