ESXi itself really does not need to be backed up as it is easy to install again. Sure there a few settings, etc ... but they are easy to reconfigure... Of course for full VM backups, it is difficult for Free Editions of ESXi.
1) You can do full backups of the VM's using the Free FastSCP (www.veeam.com) or a similar tool to copy the VM files while they are powered off.
2) The other option you could use the William's Lams' GhettoVCB script that will allow you to backup the VM's while they are running . http://communities.vmware.com/docs/DOC-8760
Hope this helps.