I'm chatting to a customer (he might even be here - Hi Simon) at the moment about how to deal with performing the MBRalign process for a large number of VMDKs. In this instance, we have 200 to deal with so could be a very labour intensive activity. I'm wondering if anyone has come across any tools or scripts to ease this process.
I'm guessing that some convoluted batch file processing on the command line might be possible btu for me that would take longer the manual conversions!
You can use mbralign with the destination datastore parameter so that it's like a migration form an old datastore to a new datastore. So only aligned VM's end up in the new datastore. Rather than running this through the ESX console, using a Linux host (or VM) can be much faster. You can also call several Putty sessions to it and just rotate sessions. If enough people get on board, each with designated VM's to "migrate," you may move quicker than you'd think.
There was a NetApp blog post recently (can't find it now for some reason) stating that you can get MUCH higher throughput by running mbralign from a Linux box rather than in the Service Console (as the Service Console is relatively resource constrained compared to a regular Linux box).
That doesn't precisely help with doing "in bulk" but should cut the time down somewhat at least (either for one-offs or bulk processing) -- given the # of VM's you're talking about, I'm betting the setup time for a couple of Linux boxes would be more than worth it.