The best SCP/FTP-over-SSH client for Windows I've encountered is WinSCP (http://winscp.net/eng/index.php http://winscp.net/eng/index.php). It comes in a standa

The best SCP/FTP-over-SSH client for Windows I've encountered is WinSCP (http://winscp.net/eng/index.php http://winscp.net/eng/index.php). It comes in a standalone install-nothing flavour and lets you choose, when copying a group of files from A to B, to only copy files that have changed. I'm not aware of what algorithm is used to determine when a file has changed. I've always assumed this is based on file modification time so this might not be clever enough to spot a partially-uploaded file and either re-copy or start from where it left off. You can certainly pause file transfers and subsequently resume but only during a session.