If you have a MSA or another SAN solution you can increase the performance of the hardware a lot with the help of the diskpart tool that's available thru the prompt. This is only for windows 2003 since windows 2008 will align the partitions by default.

1. Create the machine and the disk.
2. Mount the disk in an existing virtual machine.
3. Delete all partitions on the disk.
4. Open a promt and execute diskpart.exe
5. At the Diskpart command prompt, type List Disk and press Enter. If the disk you want to align does not appear in the list make sure that it exists and is accessible using the Disk Management snap-in.
6. At the Diskpart command prompt, type Select Disk X, where X is the number of the disk as shown in the output of the List Disk command. Diskpart should return a message that indicates that Disk X is the selected disk.
7. At the Diskpart command prompt, type Create Partition Primary Align=X, where X is either 32 or 64, depending on the recommendation from your storage vendor. If your storage vendor does not have any specific recommendations, it is recommended that you use 64.
8. Shutdown the machine and and mount the disk in the intended machine.

This is the same steps as I found in this article on Technet.