1) a sarcastic answer implying "who else would be here?" or "just the regular crowd"
2) could be used to hide someone there who should not be
source: originally from a fable involving a chicken thief (possibly a fox) hiding in the hen house and answering the farmer's question of who's making all the noise.
Also made popular by a 40's song of the same name by Louis Jordan.
Dad (coming home from work): Anybody home?
Older Daughter (in bedroom): Nobody here but us chickens! (implying herself and her sister, but is actually herself and her boyfriend, who should have gone home already)