Correct translation of French phrase

Scratch the last one altogether - it's extremely archaic.
The first is a simple imperative, literally "do what you would wish"
The second is more impersonal (using an infinitive & a non-conditional verb): "to do what you wish"
The third is the best (a quotation from Rabelais), but incorrectly spelled - it should be "Fais ce que voudras"

Fais ce que tu voudras is less formal

Faites ce que vous voudrez is more formal, or plural, but I speak a more modern french, so this may not suit.

I'm afraid I have to disagree with benbenberi. Though "Fay ce que vouldras" is archaic (it's middle French) it was the quotation from the Abbey of Thélème that Rabelais actually used in Gargantua. So, given that "Do what thou wilt" is consciously archaic, I'd go with "Fay ce que vouldras." Like the English, it's close enough to modern French that any French speaker would understand it and for anyone who knows the origins would recognise it as the original phrase.

I agree with the brass cat. There are few similar expressions, but that one is good.

What anguswalker said. If you want to preserve the archaicism of the English version, the archaic French "Fay ce que vouldras" would do it.

Addendum - "Fais ce que voudras" and "Fay ce que vouldras" would be pronounced virtually the same. The difference is the spelling.