Alan's answer is spot on.
Avoid javaScript or carefully follow best-practices so Google can crawl all content without reading javaScript. Alan is exactly right when he said: never count on Google crawling through your JavaScript to find content, but also never count on being able to hide anything from Google via JavaScript.
Whether you use PHP or not is not directly relevant. PHP is executed server-side, so Google never sees your PHP code and doesn't care. What matters is whether your programmer writes PHP code that will generate search friendly HTML code, url structure, etc.