I thought from esx4 onwards if you formatted through the viclient they were automatically aligned, only in 3 they were not.
Just checked the http://www.vmware.com/pdf/Perf_Best_Practices_vSphere4.0.pdf
The alignment of your file system partitions can impact performance. VMware makes the following
recommendations for VMFS partitions:
Like other disk-based file systems, VMFS suffers a penalty when the partition is unaligned. Using the
vSphere Client to create VMFS partitions avoids this problem since it automatically aligns the
partitions along the 64KB boundary.