You can put the boot disk of a virtual machine on a SAN-based VMFS volume.
Booting from a SAN is complex. Problems that you encounter in physical environments extend to virtual environments. For general information about booting from a SAN, see the vSphere Storage documentation.
Follow these guidelines when you place the boot disk of a virtual machine on a SAN-based VMFS volume:
Consider the best practices for boot-from-SAN that Microsoft publishes in the following knowledge base article: http://support.microsoft.com/kb/305547/en-us.
Use StorPort LSI Logic drivers instead of SCSIport drivers when running Microsoft Cluster Service for Windows Server 2003 or 2008 guest operating systems.
Test clustered configurations in different failover scenarios before you put them into production environments.