There is a commercial tool available to complete disk alignments for you. The product was a written by vizioncore it's called vOptimizer.
This product is intended to perform many disk optimisation tasks in the virtual environment, one of these is start sector alignment, in fact it's the only feature I have ever used..
I have not used the product for over a year now.. Seems when vizioncore were purchased by Quest they went from being a friendly flexible company to a difficult, rigid and unresponsive one.
I've been reading this post in preparation for checking the alignment of our guest disks, we have completed a SAN migration and I feel the command latencies are higher than I'd expect..I therefore suspect during migration there may have been misalignment introduced into what was an optimised environment..
I'm dreading having to deal with Quest support..eg. I know we paid our maintenance on vOptimiser but as expected there was never a new license file sent for the new version.. I'm sure I can blow a couple of hours with support on this alone..
I'd hoped there was another product available which could perform disk alignments in a managed GUI interface..I've not found any yet beyond vOptimizer.
I see Quest has been bought by Dell.. hmmm they couldn't do any worse.