What can you do if you do owe back rent, were evicted but you know you were evicted for retaliation?

You do not tell us where you are in the process. If the three day notice said you would be evicted for failure to pay rent, you could successfully win an eviction trial if you could prove that was not one of the reasons. If you left without an eviction trial, you could sue the landlord. But how are you going to prove that the failure to pay rent was not the cause of the eviction? Unless you have something in writing from the landlord or he told someone else why he was actually evicting you, it would be his word against your word and you have the burden of proof.