I found syncronizing a whole site awfully painful, as all directories have to be individually listed and it takes quite a long time.
The only software that I found that lists the directories in multiple sessions is Crystal Site Updater but it's full of bugs.
What software do you use the sync your site?
Some programs allow to use the MDTM command to set the uploaded file date, but Dreamhost server doesn't seem to allow it. How can I get around this problem as my file sizes also differ?