The following article recommends aligning disk partitions in guest file systems.

Recommendations for Aligning VMFS Partitions
http://www.vmware.com/pdf/esx3_partition_align.pdf

Instructions for Guest File System Alignment
Once you have aligned your VMware VMFS partitions, you also need to align the data file system partitions within your virtual machines.

Note: Aligning the boot disk in the virtual machine is neither recommended nor required. Align only the data disks in the virtual machine.

1. Ensure that no data exists on the disk. Then open a command prompt and start the disk partitioning utility.

diskpart

2. Enter the command to select disk 1.

select disk 1

3. Create the aligned primary partition.

create partition primary align=64

To verify the alignment of an NTFS volume run the following commands from a command prompt:

diskpart
DISKPART> list disk

  Disk ###  Status      Size     Free     Dyn  Gpt
  --------  ----------  -------  -------  ---  ---
  Disk 0    Online        16 GB      0 B
  Disk 1    Online      8189 MB      0 B

DISKPART> select disk 1

Disk 1 is now the selected disk.

DISKPART> list partition

  Partition ###  Type              Size     Offset
  -------------  ----------------  -------  -------
* Partition 1    Primary           8189 MB    64 KB

From the above it can be seen that the Offset is 64KB, showing that align=64 was used.

To list all partitions with a single command, run the following command from a command prompt:

wmic partition get BlockSize, StartingOffset, Name

BlockSize  Name                   StartingOffset
512        Disk #0, Partition #0  32256
512        Disk #1, Partition #0  65536

From the above it can be seen that Disk #1 was configured using align=64, where as Disk #0 was created using the standard tools (or align=32).

Recommendations for Aligning VMFS Partitions
http://www.vmware.com/pdf/esx3_partition_align.pdf

Disk performance may be slower than expected when you use multiple disks in Windows Server 2003, in Windows XP, and in Windows 2000
http://support.microsoft.com/kb/929491

Diskpart
http://technet.microsoft.com/en-us/library/cc773140.aspx#BKMK_15

Predeployment I/O Best Practices
http://www.microsoft.com/technet/prodtechnol/sql/bestpractice/pdpliobp.mspx#EPAAC