“Who made you sad” is good enough.

No. You could say "By whom were you made sad?", as you need to introduce the agent with by, but it does not sound natural at all. "Who made you sad", on the other hand, does sound quite natural and is grammatically correct. Hope it helps!

It would be possible if you added "by" and said "Who were you made sad by?" or "By whom were you made sad?". ／I'd say neither of them is natural, though.

"Who were you made sad" doesn't make any sense. "Who made you sad?" would be the correct way of asking "which person made you (the listener) sad?" However, in normal conversation, you'd more likely say "who upset you?" instead, although it would depend on the context of who you were speaking to (for instance, you might say "who made you sad" if you were talking to a 5 year old). If you wanted to ask which person the listener made sad, you would ask "Who did you upset?"