I wanted to delete all PHP closing tags (?>) from a PHP project. So I used the following regex in Sublime Text 2 to delete them. (The leftmost button activates regular expressions)
It only replaces the closing tags at the end of the file (\z = EOF).
Be sure to apply this only on *.php, and not on *.tpl files.
Slight modification for finding files without a newline at the EOF.