As pulse added the problem is related to the fact that PHP uses in some cases session ids in the url and since session changes from user to user the URL looks different at the “eyes” of a search engine. PHP pages are dynamic so you will find in most cases question marks in the url… for example : mydomain.com/showuserinfo.php?userid=222

Google doesnt seem to pay lots of attention to this since it means dynamic conent, maybe automatic information and marks that as not so relevant information. Poeple use dynamic page sto fool search engines and Google pays attention to that also.

I don’t know how much relevan or not relevant a dynamic page url (with query string) is for Google.

however if your site has good content and good links pointing to you you, good navigation you should not have problems with clean url .php pages

a php extension by itself will not hurt you… but yes, try to use clean urls. Use search engine friendly urls and try to avoid query strings as much as you can.