Those pages will eventually drop out of Google's index, but if there are still sites (either pages within your own site or others) that are linking to any of those pages you will continue to see 404 error codes. I'm working on fixing the same issue on a site that I just started optimizing.
The best thing you can do is a 301 redirect from each of the old .php pages to a similar, relevant page that currently exists on the site. This will fix the 404 codes and also pass any page authority from the old page to the new page that it is being directed to.
Here's some helpful info from Moz on 301 redirects: http://moz.com/learn/seo/redirection
Hope that helps!