As i imagine -John, I'm taking your bike. You are punished! -For what?! -Mike, could you please visit aunt Mary? -What for?

Arucard303 has it down. "For what?" implies some kind of strong disagreement or objection to whatever he is asking about. "What for?" is just a less formal way of saying "Why?". It does not imply disagreement. This is not set in stone, though. You could add or subtract emotion to either phrase to make use of it in the other sense.

I think this is just slang, and that they have the same meaning. In writing, I would use: "Why.." "For what reason..." (Possibly the origin of the slang expression)

Order of the words.

Rather "what for" has a stronger tone. Like "what do you want for me, for ef's sake!" vs. "you want me to tell you what, god damn it?!"