Here is an interesting Microsoft Knowledgebase article titled Disk performance may be slower than expected when you use multiple disks in Windows Server 2003, in Windows XP, and in Windows 2000.
It explains how a partition misalignment can cause significant I/O by causing reads and writes to straddle track boundaries. The fix is to use the diskpart.exe utility to create an alignment offset when you first create the partition.
This is similar to what you do with SAN storage to align the starting offset to “significant” boundaries. See the 3/31/08 post for more details.