Question

1. It smells bad in here.
2. It smells bad.
3. It smells bad in this room.
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What does it refer to in each sentence?

Answer 1

I take "it" to be referring to the smell, the atmosphere. In other words, the smell in here is bad.

Answer 2

Then, "it" doesn't refer to a specific thing as in the following?

e.g. How is it going?

Answer 3

No, nothing specific.

"How is it going?" is just a casual question someone might ask when meeting someone in a hallway! There is no particular antecedent for "it."