Don't do this with VirtualBox VMs either. The entire disk image is backed up by Time Machine, even if only one byte changes.
Like some others here, I exclude the VirtualBox folders from Time Machine and manually archive as necessary. Luckily, I don't rely on my VirtualBox VM instance for much; all of the key data is backed up outside of the VM disk image in manageable sizes (like less than 100MB).
I basically back up the VM disk image so I don't have to rebuild the system from scratch. I do this after substantial Windows updates so I don't have to download and install that stuff again.