Maryse gave good answers. I would like to add that you can only say "Who with?" if it is in the context of a conversation:
I went to a movie last night?
Oh, who with?
Outside of that, you need the whole question. Which question you use depends on the situation.
If you are asking about a particular time, you would use "Who were you with?"
Who were you with last night?
Who were you with when I saw you at the mall? (because of the word "when")
If you are talking about a location/event, use "Who was with you?"
You never go to movies alone. Who was with you last night?
If you were with a group, then "Who were you with?" is more common, because you were a part of their group. If you were leading a group, though, that makes you more important in the sentence, so "Who was with you?" might be the better choice.
However, for your suggestion as a substitute for a general question, it won �t work.
I hope this isn �t TMI.
Bruce