You missed the most obvious one: What is in the box? Or, if you are pointing to an item in an open box, then: What's that thing in the box?
As for your comment under Peter's answer, which asks:
So do "What's in the box?" and "What is it in the box?" have exactly the same meaning?
The don't really mean anything different; they are both valid, grammatical ways to inquire about the contents of a box. But they might be used in different situations (or contexts).
For example, If I can't see what's in the box, I'm more likely to ask: "What's in the box?" On the other hand, if I can see what's in the box but I can't recognize what it is, then I might as, "What's that thing in the box?" (or, if I'm pointing at it, I there's a good chance I won't mention the box at all: "What is that thing?")
So, there's no single way to ask a question like this:
What's in the box?
What are those things in the box?
What kind of animal in the box?
(or, maybe, if can tell it's a cat: Why is that cat in my box?)