I've been working on the server that's running this web site and a couple others and one thing high on the list was automating backups.  If you bundle backups with hosting plans, they always seem to be fairly expensive, so I choose to use Amazon's S3 service with Jungle Disk.

Jungle Disk's biggest shortcoming is the fact that you have to be logged into the console in order for backups to fire.  It appears you can run the software as a service, but I've read mixed reviews.

My solution uses standard Windows features that should work on most Windows Servers.  It uses Windows Task Scheduler with two actions, one to kill any running JungleDiskMonitor.exe process, and a second to start the JungleDiskMonitor.exe process with the --startbackups and --exit switches (you can read about them via the link above).

The reason I kill the JungleDiskMonitor process is due to this screen:

Jungle Disk seems to hate to have a second copy of itself running and when I tried to fire the Windows Task Scheduler job, I would encounter this error.  Solution, kill the process before starting Jungle Disk with the TaskKill command.  Here is the command I'm using to kill the process:  taskkill /IM junglediskmonitor.exe /T /F

Here is what my job looks like via Windows Task Scheduler:

What's nice about this solution is that I can remote into my server and open Jungle Disk and adjust my backups and settings.  From the sounds of it, if you run it as a service, you lose this ability.