My approach to backing up guest VM’s from ESX3.5 is two-headed:

• Backup the data like you would a normal machine by attaching via SMB, NFS, SQL, etc.  Just get the data
• Backup the Guest VM via the ESX host (pull a bare metal snapshot of the entire system)

Why backup everything twice you ask?

Well fortunately for you and unfortunately for me I have a real world experience that will help answer this question. I had a vm guest failure and had to rebuilt a vm then restore data and settings.  Suffice to say this took forever. So here’s why you can do both…

• If data is deleted you have backup sets that have just pure data - files that are used by applications and users. If a single file gets deleted, corrupted, or anything else _bad_ the restore for this file(s) is quick and easy.  Restoration of this file(s) doesn’t need to affect every other user connected to the system in question.
• If the OS becomes unusable, system files fail, vmdk (virtual disk) files on the host get corrupted then you now have the full machine backup to simply turn back on from date X/Y/Z. Asigra actually takes a native ESX snapshot at the time of backup.

Using Asigra Televaulting (or a small handful of other backup systems) allows us to perform backups that are compressed and bit level.  So, if I have a VM that has a 20GB vmdk disk, but really only has 8GB of data in the guest system, then the backups will actually be less than 8 because all that free space will be compressed down to nothing and then the 8GB of real data will further be compressed down.

My schedules are now setup to backup real data each night, but backup the OS (again using the native ESX snapshot) once a week.  For the most part, system settings and configurations aren’t happening each day. So, if the guest VM dies, I can simply restore the VM to the last weekly backup (as of at the most 6 days) then restore the real data to to that machine (as of at the most the night before).

A note for Asigra users - I’ve had a lot of problems backing up via VI.  So far attaching directly to the ESX hosts seems to be working great.  The one fallback for this is you need to setup rules to ensure that VM’s stay on the same ESX host.  Asigra only knows that a guest VM is on the host you originally configured it to be backed up from.