Now PHP manuals use .php (and sometimes .inc for included files).
The php3 extension comes from the past...
Really you may set up your web-server+PHP configuration to recognize any file extensions as PHP (why?)...
php3 AFAIK is just the historical reflection that there was PHP v.3.
In my opinion en experience it seems best to just limit yourself to one extension, e.g. php. A number of extensions that are parsed could decrease the servers efficiency since files might be parsed that don't have any PHP. One extension also makes clear that all other files that contain PHP will be served as plain text - careful with backup files like with EMACS, foo.php~, they could expose code.
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