'She threw the jug out of the window.'
'It was the window that she threw the jug out of.'
It was out of the window that she threw the jug.'
Are these both sentences correct?
#3, whilst grammatically correct, would not be uttered. It is completely unnatural.
I will make an argument for a version of #2 but not with "It" at the beginning. For this, read the following dialogue:
A - Mary threw a jug out of a window last night!
B - Why?
A - Oh, she was having an argument with her boyfriend.
B - Which window did she throw it out of?
A - The one on the third floor next to where the name of the building is painted.
B - I don't know which one you mean. Can you show me?
A - Yes of course. Come outside with me for a moment.
(The two go outside and A points up at a specific window.)
A - That is the window that she threw the jug out of.
Remember - if you don't use correct capitalisation, punctuation and spacing, anything you write will be incorrect.