.php is of course the most common
.phtml isn't seen much anymore, but used to be used a bunch.
.phpX where X is the major version number can be used to run the script with a particular version. For instance, you can run PHP 5 scripts by default and PHP 4 scripts for .php4 files. .php3 and .php2 are for historical purposes, since PHP v3 and PHP v2 are long gone now (hopefully)
As a side note, some people add .html to their PHP extensions, so that all .html files are processed with PHP. This is usually done locally in a .htaccess file, not globally on the server.
The default it includes usually gets most stuff you need. If you run easyapache there is an option for a typical ecommerce server or something close to that, select that and most people are fine for php modules.