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.

You can also use Net::SFTP.

not really, maybe ssh or telnet

It might be the way I'm using it...it never seems to find the file I'm working with. Not sure why

It's pretty easy to write unix format text files on your windows machine,

{
    local $\ = chr 10;
    # . . .
}
[download]

If the problem is to write your file directly to the unix box, the answer depends on the kind of access you have. I'd recommend ssh over telnet, and sftp is nice. NFS is possible, but less desirable IMO. sftp will translate line endings for you in ASCII mode.

The biggest difference is that windows distinguishes between text and binary files (it interprets the line-ending character differently for text files) while unix doesn't. See binmode and perlport.

If you want to read and write files from/to a unix machine, you can use all kinds of network protocols to send/recieve the files. Personally, I prefer to use plain scp to transfer files, since it's available everywhere, has good authentication mechanisms and is encrypted. There are also perl modules to do scp, but they tend to require a bit more work setting up, especially on windows. See for example putty for nice and free ssh & scp clients for windows.