"¿Cuáles son las diferencias?"
Translation:What are the differences?
OK, as I understand it: Que asks for an explanation, definition, description, or general info, and it precedes a verb or a noun (It asks "What?"). Cual/cuales asks more specific questions, or to distinguish one item from others (It asks "which?" even though we may translate it "what?") and is not followed by a noun. This sentence above looks like a "Cuales?" situation to me.
Usually "cual" is used before the verb "ser" except in some colloquial expressions such as "Que es la hora", or when you're asking for a definition. I found this page very helpful: http://spanish.about.com/cs/grammar/a/que_vs_cual.htm