I have been researching the ideal disk formatting for SQL Server in summary:
All DATA, LOGS and TEMPDB should be formatted using a cluster size (allocation unit) of 64k
All Programs and Backups formatted using a cluster size (allocation unit) of 4k
The exception to this would be down to the array you have chosen and if you are using SSD\Flash disks, which mandate a different configuration. i.e. Violin Flash Memory recommend formatting using 4k
These are good articles to read:
http://blogs.msdn.com/b/jimmymay/archive/2008/12/04/disk-partition-alignment-sector-alignment-for-sql-server-part-4-essentials-cheat-sheet.aspx
http://technet.microsoft.com/library/Cc966534
http://www.violin-memory.com/resource-library/#whitepapers