Update: Both almut and ig have already mentioned remote mounting. Here's some more background on doing this over ssh or ftp.
in reply to Comparing Directories on different servers
On a 'nix system, non-root users can mount remote directories as a pseudo filesystem in user space, say using sshfs, or CurlFtpFs
Both of these are underpinned by the absolutely brilliant FUSE (File System in User Space).
Once mounted, you can, for example, access the file systems from the shell. You can also use utilities such as File::Find.
If you have ssh access to the remove server, and sshfs is installed:
If you only have ftp access to the remote host, curlftpfs does the same sort of thing:
% mkdir -p sshfs/someuser@somehost
% sshfs someuser@somehost: sshfs/someuser@somehost
% cd sshfs/someuser@somehost
% ls -l # list remote files
% echo awesome\! >cool.txt # create a file on the remote server
% mkdir -p ftpfs/someuser@somehost
% curlftpfs ftpfs/someuser@somehost someuser:mypass@somehost
% cd ftpfs/someuser@somehost