I was using ESXi 3.5, and Adaptec 39160 SCSI card and a Dell LTO2 tape drive to backup our 4 VMs from inside a Win 2003 SBS server using SCSI passthrough and Backup Exec 12.5, all of which worked well. I upgraded to to ESXi 4.0 and it appears the Adaptec 39160 is no longer supported (shame on me for not checking the HCL more thoroughly). We're also moving to SBS 2008 so I am unsure what wrinkles that will add to the equation.
We are a small business, to which virtualization has been a godsend, but we're using relatively low-end hardware, with a whitebox server and locally connected SAS storage and obviously face the economic constraints of a small business. Ideally I'd like to just replace the 39160 card if that is possible, and there's something that will work with Backup Exec on a Win 2008 VM, but if that's not the best solution we could probably pony up $1-2K for a more robust/supported solution, or just put together a standalone backup server with some leftover hardware if that's the best approach. If there is a replacement SCSI card that would work, a specific model number would be very appreciated!