A good naming convention that I am fond of is calling web-page files .phtml and logic files .php
A .phtml file will signify that there is code on the page that needs to be parsed, but it is a "web page" that will be displayed in a browser.
The .php extension signifies that the file is simply code (or a shell script) to do some processing that will send the results elsewhere.
Good Luck!
-Phil