It's not a good idea for the PHP to generate Javascript. The only javascript I would recommend exporting is simple JSON assignments like the following:
<script type="text/javascript"><!--
var MyNamespace.info = <?php echo json_encode($info_array) ?>
// --></script>
This is the easiest way to sanitize PHP information and let it be accessible to javascript on the client. However, anything else should be written in actual JAVASCRIPT FILES that are referenced with <script> tags at the head of the document. The only other appearance of Javascript from server-side files, that I would say is alright, is stuff placed into "onclick" and other such attributes.
The rationale for this is that the Javascript should be written and maintained by front-end people who know Javascript, and the site should be able to work (at least partially) without javascript. There is no reason to generate spaghetti Javascript inline.
Check out my PHP framework, PHP On Pie (
[To see links please register here]
) for an example of how to implement this properly. It keeps the JS and PHP separate, except when exporting JSON as shown above. However it also provides conventions for easy interoperation between the client and server via AJAX.