I believe this can be done over samba using open, ftp using Net::FTP, ssh Net::SSH, or even telnet Net::Telnet — and all from perl. Did you have a preference? I think "best" is probably a subjective evaluation which depends on the tasks and environments at hand.

UPDATE: File::Remote looks pretty slick to me. I might even try to use it later today. Is there any particular reason it won't work? It appears to use rsh/ssh as instructed and might be a pretty clean way to do it.