Answer from Edwin Yuen, Microsoft Virtualization expert:
Functionally, they are the same. Both provide the capability for unplanned downtime, with the automatic failover of a VM between nodes. One difference is that Windows Clustering allows a wider range of configurations and hardware compatibility since it leverages Windows.
If comparison had to be done, it would have to be done at the different layers. VMware’s HA is identical to have a hardware load balancer to protect the whole virtual server component while Microsoft’s Clustering is at the application layer to protect an “application like Exchange and SQL not too much the hardware itself.