At an EMC class I took recently, the instructor claimed that in testing she had done, correctly aligning the partitions on a physical Windows server resulted in 30% performance gains. I'm not sure what, if anything the gain is for aligning the partitions in virtual disks, assuming the underlying VMFS LUNs are aligned (which by default they will be if they're created under ESX 3+ or vSphere).
That being said, this is the advice from the "Performance Best Practices for VMware vSphere 4.0" guide:
Make sure the system partitions within the guest are aligned. For further information you might want to
refer to the literature from the operating system vendor regarding appropriate tools to use as well as
recommendations from the array vendor.
This is a potentially useful tool -- a powershell script to check the partition alignment of your Windows VMs. (via Scott Lowe )
I haven't adjusted the partition alignment on my Linux VM templates yet. That's on my To Do list, hopefully for some time in the near future. I plan to do some before and after performance testing, and I'll post the results here when I do.
