"I don't know what is that"
This sentence is a bit strange and needs punctuating, but or is otherwise fine. Agreement-wise 'that' is singular, do you need to use the singular conjugation; is. The following makes total sense:
"I don't know, what is that?
"Do you know what are the examples?"
In this sentence, again, the agreement is fine; the word 'examples' is plural so you use are. The one thing you do want to change, is the word order. Because it is a question you swap it around, do it should look like the following:
"Do you know what the examples are?"