Hi Fred,
It depends on what you want to accomplish really.
1. If you want to be able to restore files and folders out of it, this would be the best way to do it. You would only need a Remote Agent license for that particular server along with whatever agent is required (eg. SQL, Exchange, Lotus Notes etc.). It's possibly also the cheapest way of doing this in terms of cash outlay. In this scenario, you'd want to back up the server's System State, and any other system folders/files deemed necessary. That said, recovering the server would take longer...you'll have to install a new VM, and then run the restore to bring it up-to-scratch.
2. I wouldn't bother with this option myself.
3. License the VMWare agent in Backup Exec and use this to backup your servers. THis would allow full backups of the VM, and restores down to a file level out of it. It might cost more in terms of licensing, but if you ever had to restore the entire VM, it would mean less work. You would simply restore the whole VM and that would take as long as your hardware allowed it.
Hope this helps?