Backup is hot topic when discussing your vCloud Director architecture setup. Until recently there was no real integration with vCloud Director and most backup vendors. Most of them could backup vCloud vApps, but did so without the metadata that is required to restore the vApp in the vCloud (i.e. which organization, which organizational vDC, etc.)
Over the last period several vendors have come up with an vCD 5.1 integrated solution, which is of course great for everybody running vCloud Director.
More information on backing up vApps for vCD Tenants can be found in the VMware whitepaper here.
Most backup products use vStorage API for Data Protection (VADP). VADP uses snapshots to create backups of running virtual machines in a vApp. This is were it becomes challenging. vCloud Director 5.1 will only support one snapshot (see here for more info).
So what happens when VADP takes a snapshot?
The snapshot action by VADP will commit the already existing snapshot of the virtual machine. This results in a single VMDK being backed up to the backup solution. In the event of a restore the backup solution will restore the consolidated virtual machine. The last state known, but without the snapshot.
Take this into account when designing your vCloud Director backup solution. Ask your backup solution provider what the backup solution does in the event that it recognises a snapshot. For now it would be better to skip / create a warning in the event of snapshot detection within vCD.