It's all really a matter of scope I think. Of course, the friendlier a package is to Perl and the harder it would be to replace, the more likely it'd stay around anyway. Apache, postfix, Exim (although I prefer Postfix), emacs (although I prefer vim), vim, the GIMP, and several others already are pretty Perl-friendly.
Startup and shutdown scripts would definitely be the place to start. The reason I'd like also to see many command-line tools done in Perl is threefold. It encourages more tinkering than the current BSD or GNU tools. It also, if they are licensed under Perl's terms, deals with quite a few licensing issues where BSD and GNU tools fall on opposite sides of the fence. I could take my Perl-based, Perl-licensed tools anywhere on any system where they'll work, and not get hassled by others about the license. It's also a bit easier to have portable Perl-based programs for the command line than to write similarly portable ones from scratch in C. Most of the portable C programs that exist got that way over a long period of time.