How to use the question mark in multiple choice questions?

Which one of the following three forms is correct for a multiple choice question?

Do you prefer the blue dress? or the red shirt?

Do you prefer the blue dress or the red shirt?

Do you prefer the blue dress? or the red shirt.

The first form seems the most syntactically adequate, as both "blue dress" and "red shirt" are equal options of equal value in the sentence.

The second form also seems adequate, as the question mark is marking the entire sentence as a question. However, it is ambiguous whether "blue dress" and "red shirt" are two separate choices, or "the blue dress or the red shirt" is a single choice.

Finally, the third form is the one that represents the spoken form most accurately. However, it looks somewhat strange for a question sentence not to end with a question mark.

You only need the question mark once, at the end of the sentence. While the two clothing items are separate, they're considered together in this context. "do you prefer the blue dress, or red shirt?"

The purpose of commas is not to suggest places where those reading aloud might want to pause, but to help readers understand the structure of a sentence. If they do not help the reader in this way, then they serve no purpose.

In a sentence such as ‘Do you prefer the blue dress, the black coat or the red shirt?’ the comma after ‘dress’ is what R L Trask called a listing comma. His advice would be not to put another after ‘coat’, because the word ‘or’ already indicates a further, and final, alternative. The same logic makes any comma in your example equally superfluous. As Trask says ‘Put a listing comma before and or or only if this is necessary to make your meaning clear.’

The kind of punctuation shown in the first and third versions of your example is distracting, confusing and unlikely to be used by any reputable publisher.