If I understand correctly, PHP only runs on Web pages. The Perl Debugger and the ability to run interactively means you can more thoroughly test and debug programs.

Perl programs can run as daemons, background processes.

The huge number of libraries in CPAN mean a Perl programmer can do credit-card validations or statistical analysis, produce graphs, perform date validation or calculation, or manipulate Word documents / Excel spreadsheets / XML files, produce documentation from comments, or ... out-of-the-box.