This has been an "issue" ever since I started using PHPEd but I decided to officially ask for it.
Would it be possible to remove the last CRLF from the template files for PHP?
Using one of these templates will always result in the output of an empty line, which is not what you want.

I know it's not really an issue and easily fixed, but we all want PHPEd to be as perfect as possible, no?

Agreed. Another minor annoyance of mine with the default PHP5 template is the first-line of code is indented 2 spaces - not even 4 spaces or a tab! So I always have to remove that indent, and re-tab the line in.

I've edited both of these in my local template but I agree it could be done by default.

not at all
if you check php grammar, you'll see that closing tag may contain \n. In other words, line end after ?> will always be swallowed and will never apppear in the output.