What's the difference? When do you say them?
Where did the time go? and Where has the time gone?

Question

What's the difference? When do you say them?
Where did the time go?  and  Where has the time gone?

Answer

They are both the exact same in my opinion, you could use either and there is no difference. Both phrases are used to show how surprised you are at how quickly the time has passed.
Ex: 
You meet your friend for a coffee. After a while you check your watch and are surprised to see that you and your friend have been chatting for 2 hours and you are now late for work. You could then say 'Oh god, where has the time gone? I best be off, I need to be in work before 6pm'.

Answer

There's no difference. You say them when you are surprised that time has passed so quickly.

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