In a "Rose for Emily," what was the smell that was referred to in section II. Was it Homer or her father? Please explain why.

In the short story "A Rose for Emily," the reader is not told what the smell is that is coming from Miss Emily's home.  It cannot, however, be her father.  Emily's dad passed away two years before this smell occurred and although she would not at first let anyone take her father's body, she did eventually relent to having him buried.

The reader can however infer that the smell is from the rotting body of her male friend, Homer.  Since he has disappeared, has not been seen, and shortly thereafter a rotten smell comes from her house, we are pretty safe in saying it is the decaying body of Homer. She wouldn't have told anyone because she was not about to have him taken from her.