At first sight both expression can be used interchangeably. I heard that "as you want" is sexually connotated (UK). Is it right? As a consequence I have become reluctant to use "As you want" in the traditional sense of "whatever you want".
"As you wish" is better usage than "As you want," but you have to be cautious, because "As you wish" can be construed as being sarcastic by the listener unless it is very carefully spoken. If you are speaking with a client, saying "As you wish, sir!" (or "As you wish, madam.") would lessen the likelihood of your response being misunderstood.
On the other hand, if you intend it to be sarcastic, then saying it with a flat tone and offering a weak smile will convey your disdain for the person.