If someone ran past me in my house, I'd yell, "Stop thief!" Or "Help! Police" If I was home and heard a noise in another room, I might say "who's there", and if I came across somone in my house, I would say, "Stop. Who are you and what are you doing here." Of course, as a man, I would probably knock him out first, then ask questions later. (Don't mess with Texas!)

If someone was already in the house and quite clearly a thief, I would yell "Stop there!" or "Stop thief!" or maybe even just yell. (I would probably dial the police or 911 as well-- I'm not quite as equipped or as ready to knock someone out.) However, if it was someone in the next room that I couldn't identify, I would say "Who's there?" or "Who is it?" However, it seems like "who is it" is more used for someone at your door. "Who's that" is used if you were asking someone else who the third person was.

who's there ? I just guessed