Using standard modules should be more portable than external apps.

File::Copy is portable to every OS perl runs on as far as I know, while cp and copy are not available on every OS. I tend to use File::Copy for all my copying needs.

On the other hand, I've worked on some solaris installs where Sys::Syslog was not available. YMMV.

In general, using modules is faster than forking off an external program, especially if you call a lot of them, but some external programs are more efficient than the equivalent perl module, especially when dealing with huge files.