The usual form is "who paid you", because we usually do not use inversion when the question word is the subject (rather than object). The option with "did" is possible, in which case it is used to emphasize either (1) a yes, as opposed to an expected / proposed no, or (2) the simple past tense (as opposed to some other tense or aspect.

There's no difference, but the second one is correct.

Without any context, it's a bit hard to know what it is you are trying to say. In the first one, you are using the emphatic "did" which stresses the verb. Therefore, "Who did pay for you?" sounds like there was a situation where someone couldn't pay a bill and the person asking never knew what happened until finally one day realizing it he says "oh yea! About that.. who *did*pay for you, because I never found out". Your second example is a more direct question, using the indicative, simply asking the question of who paid for someone's bill/ tab. I hope that helps.