They have different meanings. A native speaker will use each form in the correct context. Time to consult a grammar book. - What did you do? (What did you <verb bare infinitive>?) Simple present. Question form for a completed action during a completed time period. - What have you done? (What have you <verb part participle>) Present perfect. Question form for a completed action during an incomplete time period ending in the period. - What had you done? (What had you <verb part participle>) Past perfect. Question form for a completed action during a completed time period prior to another event in the past.

the most common phrase is " what did you have" or just " did you have" we hardly use the first two forms in conversations.It's too complicated...