If your server is actually still using php3, then probably go with the php3 extension just so you know later the script was written for php3. Most hosting companies setup the server to parse files with both php, and php3 extenstions (some will even allow .phtml). If it's your server (not through a hosting company), then I don't see any reason to still be using php3, and thus you should write all of your code for php4, and use a regular .php extension. If you're using a pre-made script, that was written back in the days of php3 you still might want to use the .php3 extension just so you know it's php3 code.
Really it's all up to you... it doesn't really matter, especially if you're the server admin.
