360works has SafetyNet:
This uses Amazon's cloud to backup.
The other option you can use is to run a batch file after your local backup that copies files from your backup folder to a local virtual drive. I've used this in combination with an SFTP solution called expandrive before.
You could try CrashPlan Pro for Business (or enterprise). There is an option to prevent backup of live files which may result in corruption, and also the capacity to create multiple backup sets (different folders etc). Several of my clients use this program for both onsite and offsite (cloud) backups. One of your backup sets should include the "Backups" folder in FileMaker Server. There seem to be problems however with including the "Progressive Backup" folders, so without doing further testing I would suggest that you don't include that folder. It is well priced and allows unlimited backup.
You can only send files that are in the backup folder since FileMaker will have the live files open. I use DragonDisk as it is open source for both OSX and Windows. Through scripts I archive the backups to a file using 7zip on Windows and Tar/gzip on OSX and then call DragonDisk (with command line options) to do a S3 sync between the archive files and Amazon's S3 service. You can specify have many backups to synce and all sorts of goodies. I use the folders that FileMaker Server created for each backup as the archive name. This also makes it super easy to restore and get a copy since it's only a single compressed archive that needs to be downloaded.