Does anyone have preference with one over the other? Is there anything better about Perl than PHP? I know PHP well, but was considering learning Perl is it is worth it.

I have only used PHP myself but never found anything that couldnt be done in PHP that could in Perl.

I think it depends on the code you already have at your disposal. I have some sites using Perl mainly because I could find the scripts I wanted for them written in that language already.