Since you emailed me with the same question, I'll post my response:
Yes, Yummy can do this.
You'll need to install the Growl notification system, which Yummy FTP interfaces to:
http://www.growl.infoOnce installed, the Growl notifications can be set up for a completed upload, either using a window on-screen or an email
In Yummy:
• Select 'Show Queue Drawer' from the View menu
• Drag the files/folders to upload to the Queue at the bottom of the Browser window
• Select all the items in the Queue and then click the Clock icon in the top right of the Queue Drawer. This will allow you to specify the time to upload