My rule of thumb these days for choosing between PHP and Perl is that if I find a well-designed, secure, fully functional open source project written in PHP for which there is no Perl equivalent, I'll customize the PHP project. If the available starting points are equivalent or I'm writing from scratch in either language, I always choose Perl over PHP. I learned Perl first and then PHP specifically to leverage existing code, so perhaps that has something to do with it.

Sometimes I choose other languages over Perl, too. Where a language is implemented often has a big influence. Languages available on the client side of a web application, like JavaScript in the browser, ActionScript in a Flash client, or haXe (which can target either of those) are one example. Many programs use Python, some dialect of Lisp, or some dialect of Basic for plugins or automation scripting. The GIMP uses Lisp and OpenOffice.org uses what they call OOoBasic for example.

Most of my applications are web-based, but not all. Many involve more than one language. That's true for desktop apps, but especially true of web apps. Having Perl on the server and JavaScript on the client really isn't a bad combination.

I also use C, bash, Pascal, Forth, various forms of Basic, or Lisp for maintaining programs already written in those. I sometimes use C, Forth, or Lisp just to keep my hand in and teach myself more about programming with them, as I don't use them very often. Those skills are too handy to let atrophy.