Well, firstly, Fusion 3.0 just seemed to be much slower at taking snapshots and restoring VMs. Given that is what I'm doing 90% of the time that was a problem.
There seem to be two fixes that at least help, if not resolve the problem
1. Remove the VM directory from Spotlight indexing
Easy enough to do on System Preferences > Spotlight > Privacy
Click on the "+" and add your Virtual machine directory into the Privacy list.
2. Stop VMware for starting an index
Seems that VMWare causes a re-index scan to occur, so lets turn that off!
defaults write com.vmware.fusion PLLibrarySpotlightSearchDone -bool YES