Only you/your_company can determine what is or isn't needed in a backup.
If you have the backend storage to support backing up everything, then back it all up...better safe then sorry. If you have limited resources or backup windows, then you'll have to work out a scheme of what files/partitions/databases need backed up, when, and how (full, incremental, differential) as well as when those backups get overwritten (retention periods).
With VMWare and BUE you can use individual agents and backup at the VM level itself or you can use the vmware agent and backup at the vmdk level (and still have the option for individual file restores depending on setup/configuration).
Honestly though, it's difficult for us to speculate on your environment without knowing it well.
UPDATE: regarding vmware 3.5. It's not on the SCL for BUE 2012, 4.0 or higher is required to use the vmware API/agent itself. It also requires a minimum of the "standard" license as the free version doesn't include the right API for the agent to work. You can still use the windows agents inside the VMs though (assuming the OS' themselves are supported on the SCL)