Casiopea said:1. Who is it ? It is Tom. (refers to both she and he)
"it" stands for both genders 'he' and 'she', and it's especially used when the speaker cannot see the person. By the way, people also use "Who is this?" when speaking on the phone or when pointing to a person in a photograph.
2. Who is he ? He is Tom. (male, diectic)
"he" refers to a third person and it's a diectic pronoun, which means, not you or me, the people talking, but the other person, male.