Most of the file synchronization tools support FTP, some also support SFTP and/or FTPS for secure transfers. there was a recent, long thread discussing SyncBackSE and Super Flexible File Synchronizer:https://www.donation...ex.php?topic=10657.0
SyncBackSE does not support SFTP yet, with the developer looking into possible future solutions, but no firm commitment. I don't know what the SFFS story is for secure transfer.
If you have a synchronization tool that you like that does not support FTP or SFTP an alternative is something like one of the following that will map drives to network storage:
If you're dealing with a work computer situation, one thing to test before you buy is support for proxy transversal if you need that at work. In my situation, I was unable to get SFTPDrive to connect to some hosts. Jungledisk works fine (but it only has one host to deal with). I have not tried WebDrive. If you buy SFTPDrive from their site, you get a free, non-expiring 3GB SFTP account at joyent.com. So for about the price of a USB drive, you get about equivalent storage that you don't have to keep in your pocket! The support forums for both SFTPDrive and Jungledisk are actively monitored by the developer.
I'm using Jungledisk right now for a situation similar to what you're talking about, and it works great. I do have to pay Amazon a whole $0.08 (that's eight cents) a month for the S3 transfer & storage fees.