Difference between application/x-javascript and text/javascript content types

text/javascript is obsolete, and application/x-javascript was experimental (hence the x- prefix) for a transitional period until application/javascript could be standardised.

You should use application/javascript. This is documented in the RFC.

As far a browsers are concerned, there is no difference (at least in HTTP headers). This was just a change so that the text/* and application/* MIME type groups had a consistent meaning where possible. (text/* MIME types are intended for human readable content, JavaScript is not designed to directly convey meaning to humans).

Note that using application/javascript in the type attribute of a script element will cause the script to be ignored (as being in an unknown language) in some older browsers. Either continue to use text/javascript there or omit the attribute entirely (which is permitted in HTML 5).

This isn't a problem in HTTP headers as browsers universally (as far as I'm aware) either ignore the HTTP content-type of scripts entirely, or are modern enough to recognise application/javascript.

mime-types starting with x- are not standardized. In case of javascript it's kind of outdated. Additional the second code snippet

<?Header('Content-Type: text/javascript');?>

requires short_open_tags to be enabled. you should avoid it.

<?php Header('Content-Type: text/javascript');?>

However, the completely correct mime-type for javascript is

application/javascript

http://www.iana.org/assignments/media-types/application/index.html