NetLoad allows specification of a whole host of settings for each Web Site. Turn off the deletion of files and directories on the server, or be prompted before deleting. Have it delete files marked for "Refresh" before uploading the new file. This is very handy; with other FTP clients I have seen one file that does not get updated for whatever reason. The FTP client says it was updated but when viewed with a browser it is unchanged. I have had to manually delete the offending file on the server and then upload the new one. NetLoad can automate that whole process. And many other settings can be specified.
Many automatic settings can be specified in NetLoad. Have NetLoad connect to a certain Web Page on startup each time or automatically "compare" sites after login. Have NetLoad start transferring files immediatly after doing a "compare" or have it exit automatically when complete. If you have a server in another time zone, the update times won't match. NetLoad includes the ability to set time zone adjustments based on GMT. Sounds can also be associated for each action. NetLoad can also generate transfer logs for both downloads and uploads.
There are many FTP clients out there but if you have a web site you maintain on a regular basis, check out NetLoad. It's fast and will make those updates as easy as a button-click. An evaluation version is available from their Web Site, giving you 50 free transfer sessions. After that you must register.