In times of post-constructionist theories, everything’s possible, nothing is wrong, we can talk about everything, and all depends on personal preference and liking. If you’re asking me, I’d generally prefer “What’s on your mind?” and leave any other possible form to pre-constructionists.
“What’s in your mind?” sounds unnatural if you want to ask “what are you thinking?”. I’d use “what’s on your mind?” or “what do you have in mind?” which in this case means “what do you want to do?”. In some of your examples of “What’s in your mind?” usage, in context, they are appropriate.
You could begin by telling the poster that a search of both the BNC and COCA for the question What’s in your mind? (as well as What is in you mind?) results in this this response:
(From there, you could go to Google, look for examples of “What’s in your mind?” and analyze those. Judging from your previous post, however, it looks as though you were unable to find any examples of that question that were worthy of your analysis.)
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To me, “what’s in your mind?” is equivalent to “what do you see in your mind’s eye?”. Personally, I’d avoid using it completely.
To answer the original poster, I’d say don’t use “What’s in your mind?” as a stand alone question. In context, it’s OK, not by itself because like I said, it sounds unnatural even though I’d understand what you mean.