I work on Windows, but I run the code on remote Nix. Usually copied files through Winscp. I would like to know what are the alternative ways to upload files to a remote machine?
yes a lot, the same ftp, scp (by the way, what is wrong with Winscp?) samba, vpn + samba ...
rsync under cygwin. It is enough to write a simple script once. Plus, only what really changed is copied.
As an option, sshfs. Cheap and angry.
Alternatively, use ftp or svn, via cifs (smb), putty has a tool for sending files via ssh. You can organize a reverse access - make a ball on Windows and mount it where you need it in unixes. I can not imagine what suits you better. never like doing.