The SQL Server Customer Advisory Team (SQLCAT) have published a white paper on the topic “Disk Partition Alignment”. 

“Disk partition alignment is a powerful tool for improving SQL Server performance. Configuring optimal disk performance is often viewed as much art as science. A best practice that is essential yet often overlooked is disk partition alignment. Windows Server 2008 attempts to align new partitions out-of-the-box, yet disk partition alignment remains a relevant technology for partitions created on prior versions of Windows.”

Download the white paper from http://sqlcat.com/whitepapers/archive/2009/05/11/disk-partition-alignment-best-practices-for-sql-server.aspx