Disk alignment is a known problem in virtual environments. Older guest OS (primarily Windows before 2008 tho *nix has the same issue) would start their partitions slightly off the boundary which could cause an increased amount of IOPS.
You can find application guys talking about it outside of VMware but due to the consolidation factor it is a common pain point, especially for environments that use P2V of existing servers. If you build a new VM you can make sure the partition is aligned, but until recently in a VMware environment you needed to use 3rd party tools like vOptimizer or storage vendor-specific tools like mbralign to correct the problem.
VMware to the rescue.
The latest version of VMware’s P2V Converter tool includes:
Optimized disk and partition alignment and cluster size change.
So now, when you virtualize an existing Windows 2003 server (the #1 source of misaligned disks) the VMDKs created will automatically be aligned.