You first need to think about what you want to say as a simple statement rather than as a question. Once you get that right, you can convert it to a question.
You called me (simple past - before now)
This means that you called me some time before now
You had called me - (past perfect - before some event in the past)
In your situation, the first is the correct statement.
No let's look at how to turn it into a question. If the main verb in the sentence is be or a modal like can or must, or there is an auxiliary verb like have or will in front of the main verb, you just switch the word order:
You are ready. -> Are you ready?
You have eaten -> Have you eaten?
You will eat -> Will you eat?
In all other situations, you can to use Do?
You called me. -> Did you call me?
You can also ask a question just using inflection:
You called me?
Looking at your examples, you will see that the first (using Did) and third (inflection only) are correct.
The middle one would be correct if you were asking whether he called you before some event in the past (had is an auxiliary verb so you don't need to use Do), but it is not appropriate for this situation.