I just have a batch file that does it for me. Calls out to the DOS "ftp.exe" program. I manually edit the batch file whenever I need a change in behavior (which hasn't been necessary for months). It's actually rather advanced, so that essentially double clicking on the icon does the synching for me.

I don't keep lots of different folders in synch, though. Although I have considered making the batch file advanced enough to do this, and I know I could do it, I haven't bothered. Instead, what I do is maintain two folders each on my home and work PCs:

\TaxiToWork
\TaxiToHome

I just put the files I need to synch into the appropriate folder and hit the icon. My batch file calls out to WinZip to zip the contents and put them in the "synch" location as "taxitowork.zip" or "taxitohome.zip". Within the batch file I choose the direction as well as the synch location (right now, that's either my web site or my empeg player). It builds the FTP script on the fly and even does a little bit of error checking.