You can use rsync similar to scp.

Example

$ rsync -avz tux@remote.org:/home/tux data/tux

Backup Documents to iDisk

Example found at http://feeds.macosxhints.com/~r/macosxhints/recent/~3/343605459/article.php

echo `date` > $LOG
echo "Starting copy of Documents to iDisk..." >> $LOG

rsync -a -E -4 -u --exclude=.DS_Store --exclude=.TemporaryItems --exclude=.VolumeIcon.icns --exclude=tmp --exclude="Virtual Machines" --exclude="Virtual Machines.localized" --stats --progress /Volumes/"Macintosh HD"/Users/MyName/Documents/ /Volumes/iDisk/Documents/ >> $LOG

echo "Backup of Documents to iDisk complete..." >> $LOG
echo "" >> $LOG
echo `date` >> $LOG

exit 0