This issue arises because we have a nominal clause (sometimes called content clause, noun clause, etc.) that is introduced by an interrogative pronoun and includes a predicate nominative (PN). (Please look up those terms if you're not familiar with them.)
Because the pronoun introduces the clause, it comes first. If it is the clause's subject, then we can simply follow it with the verb, and the PN comes last. This works even if the verb is passive. For example:
Without passive: I know who became Superman.
With passive: I wonder what is called "the Big Apple".
However, if the pronoun is not the clause's subject (because it is the PN), then the subject comes next, and the verb comes last. This also works even if the verb is passive. For example:
Without passive: I know who Clark Kent became.
With passive: I wonder what New York is called.
(By the way, the nominal clauses in these sentences function as direct objects, but all of this is true even if the clause functions as a subject, appositive, etc.)
Now let's look at your sentences:
I asked who was the winner.
I asked who the winner was.
In the first sentence, we have standard word order: "who" is the subject and "the winner" is the PN. In the second sentence, "who" is the PN and "the winner" is the subject. Both are correct, but the meaning is different. However, the difference in meaning is actually very minor; after all, "to be" implies that the subject is the same as the PN.
"I don't see what you are looking at." is an entirely different issue, because there is no PN in that sentence. If you have any questions about that sentence, then I recommend posting a new question.