Besides the file extension I was wondering if there was any real difference between the two. Such as speed, future PHP 5 support, etc...?

There is no difference - PHP parses both file formats the same. It's kind of like how .php is the same as .php3 and .php4, etc.

One interesting thing though, is that some PHP frameworks use .php files as the main core functionality, and .phtml as template files. There is no difference in parsing, but it helps keep the purposes separate.