From what I've read,
SE's are much slower when the pages end with a .php extension, especially with query strings attached.
Also, when SE are directed to
http://www.xxx.com/ they first check to see if index.html exists, if not, they check for index.htm, and then index.php.
I personally avoid using both index.php and index.html in one directory. I'd also rename anything .php that isn't a pure script page into .html or .htm. They do get indexed much quicker that way.