This is where a sector-by-sector backup program shines.
I don't know what to recommend on the Mac, but on Windows, ShadowProtect is pretty wonderful. It backs up only changed sectors - update 10MB in a 10GB file and it only copies that 10MB - and it's insanely fast.
Even with a file-by-file backup, one thing you can do for VMware images is to take a snapshot. After you take a snapshot, further changes to the VM don't go into the large .vmdk file you just snapshotted, they go into a new, potentially much smaller .vmdk file, so your next incremental backups may be much smaller.