The usual interpretation of "Which car is yours?" puts "which car" in the subject position.
That gives the indirect question in 2. (Can you tell me which car is yours?)
However, this is an equative sentence (X is Y), and there is often an
interpretation of such sentences which puts the last element ("yours")
in the subject position.
That gives the indirect question in 3. (Can you tell me which car yours is?)
It's a matter of interpretation: Does the original direct
question ask for an answer of the form "That one is mine" or an answer
of the form "Mine is that one"? Only the speaker who asks knows
what is in his mind when he asks!
Note the difference:
-- Look at all the cars. That red car is Barry's car. That black one is Steve's car.
-- Can you tell me which car is yours?
-- Yes. The blue car is mine.
-- Look at all the cars. Barry's car is that red one. Steve's car is that black one.
-- Can you tell me which car yours is?
-- Yes. Mine is the blue one.
CJ