The first is the most likely and natural.
The second, for me, would be "What was the strangest thing you had ever seen?" or, possibly, "What was the strangest thing you ever saw?"
The third is very unlikely.
As far as the responses go, bear in mind that most native speakers wouldn't necessarily bother repeating the verb, no matter what it is.
What is the strangest thing you've ever seen?
A cow stuck in a tree!
What is the strangest thing you've ever seen?
I once saw a naked man eating a bagel in a coffee shop.
What was the strangest thing you ever saw?
Last week, I saw a UFO!
(Edit: The third option, with "was" and "saw" is unlikely in BrE but I think it might be more common in AmE.)