Punctuating "What are you going to do, sue me?"
For example:
What are you going to do, sue me?
Is that correct? Or is there supposed to be a question mark after the first question:
What are you going to do? Sue me?
It seems like "Sue me?" is not a complete sentence. Did I have it right the first time?
"What are you going to do sue me?" seems too abrupt though; shouldn't it have a comma?
A comma indicates a brief pause, or delineates subordinate or relative clauses within a sentence.
Speech tends to be more informal – you can certainly use a comma as per your example.
You could also use a dash like so:
What are you going to do – sue me?
See http://oxforddictionaries.com/words/dash for more examples.