Someone already mentioned rsync, and that's probably one of my most useful tools. One person mentioned using scp a lot. The benefit of rsync over scp is that rsync will only transfer the parts of a file that have changed. So if you run scp to sync between two computers, every file in your list will transfer, whether it has changed or not. If you use rsync, any files that have not changed will not transfer, and if all you changed in a file was a period to a comma, only that change will transfer on that 1 gigabyte file. Pretty cool.
To ensure the files transfer securely, 'rsync -essh' will make it use the ssh protocol and encryption. 'rsync -avvz' will send it in archive mode (the a), maintaining permissions, ownership, date/time stamps, etc., and will make it verbose so you can watch what is happening (the v's), and will send it in a compressed format (the z), saving time and bandwidth.