Go Google for surveys on Perl and PHP usage. Perl CGI usage and mod_perl usage are both growing according to several recent ( read: last month and this year ) surveys I found. It's not growing as much as PHP, but its growing.
Also, as noted, Perl is included in a ton of Linux and Unix/BSD installs by DEFAULT. Perl is def. here to stay in Linux/Unix/BSD environments for quite a while.
Also, for YEARS, Perl has been a great option for web scripting, mod_perl continues to develop and make it an even better option. TONS of sites are created using Perl... and all those sites need to be maintained. In my experience, it is VERY seldom that a business is willing to take an application they've dumped TONS of money into, and totally scrap it and rewrite it in another, unfarmiliar and younger language. Someone has to maintain those sites, and build on them in the future.
The fact that PHP is created by a for-profit company can also be a turn-off to many companies... what happens if someday the next version of PHP becomes closed-source? If you suddenly have to pay for it?
In any case wmac, I highly doubt you'll ever reach a point using either language where you have to worry about the speed of just including a header and footer, or even a ton of files. I'm not advocating Perl, and I'm not advocating PHP, but I would encourage you to realize that either is an option. If you want a real answer, you should go out and benchmark it both ways.
Oh, and just because a University ( Hehe, and WOW, 7 of them, Oooh! Do you have any idea how many universities there are in the United States alone? THOUSANDS! ) teaches PHP instead of PERL doesn't mean Perl is dying... I know of several universities who teach .NET specific C++ instead of standard C++... does that mean C++ is dying and .NET will dominate the world? Of course not, for a number of reasons which I won't even begin to go into. I also know of several major univrsities who teach QBASIC and BASIC... says a lot for Universitites doesn't it? And just because all the people you know don't like Perl... doesn't mean its not an appropriate solution or that it's dying either. It just means that a lot of the people you know don't like Perl. I don't like flat-panel monitors... neither do my friends, does that mean they're dying? I don't like cats or dogs either, are they going to disappear from the face of the earth too?