For me, iWeb's biggest shortcoming is that when using it without .Mac, you much republish the entire site after each change. This gets you twice, once when you "publish to folder" from iWeb, and then again when you have to upload that whole folder to your site.
Since every file is rewritten to the folder, modification dates are useless for use with an FTP program that supports syncing.
But if you have a webhost or server that you have shell access to, and the host runs rsync (most unix-based hosts should have rsync installed), then you can use checksums to only send files that are different. All you need to do is use rsync with the -c option. If you are removing files, you may also want to add the --delete option. For example:
rsync -avc Sites/mysite/ username@webhost.com:webroot/
I still have not found a way to convince iWeb to only output the changed files to the folder, but this at least gets you out of numerous unnecessary uploads.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20060521163026509