There is another way to approach this if you are using Git for source control. Inspired by an answer here, I wrote my own filter for use in a gitattributes file.
To install this filter, save it as noeol_filter somewhere in your $PATH, make it executable, and run the following commands:
git config --global filter.noeol.clean noeol_filter
git config --global filter.noeol.smudge cat
To start using the filter only for yourself, put the following line in your $GIT_DIR/info/attributes:
*.php filter=noeol
This will make sure you do not commit any newline at eof in a .php file, no matter what Vim does.
And now, the script itself:
#!/usr/bin/python
# a filter that strips newline from last line of its stdin
# if the last line is empty, leave it as-is, to make the operation idempotent
# inspired by: https://stackoverflow.com/questions/1654021/how-can-i-delete-a-newline-if-it-is-the-last-character-in-a-file/1663283#1663283
import sys
if __name__ == '__main__':
    try:
        pline = sys.stdin.next()
    except StopIteration:
        # no input, nothing to do
        sys.exit(0)
    # spit out all but the last line
    for line in sys.stdin:
        sys.stdout.write(pline)
        pline = line
    # strip newline from last line before spitting it out
    if len(pline) > 2 and pline.endswith("\r\n"):
        sys.stdout.write(pline[:-2])
    elif len(pline) > 1 and pline.endswith("\n"):
        sys.stdout.write(pline[:-1])
    else:
        sys.stdout.write(pline)