One of the nice things dreamweaver does is when you hit sync gives you a list of what files its going to move so you can check they look about right. I don't personally trust timestamps alone to do this kind of thing. I'm fortunately in the position where the only site I maintain only has six subdirectories so copying things manually isn't that hard. And I can queue files to be batched all at once for if I have files that are dependant on each other. :)

Smart FTP is what I use currently for the record. About twice a year. :)