Q: Should the disks that you are backing up to be aligned?

A: In short, yes.  The LUN or disk which hosts the backups is probably the disk which needs the most write performance.  I say this because while the database is sitting there cranking along getting all it's new pages, the full backup needs to be taken of the database on a pretty regular basis, either daily or weekly.  So unless your database has a 100% data change rate per day, the backup disk will have more data written to it per day than the normal database LUNs will they.  And all this writing is being done during a very short period of time.  After all the full backups probably only take a couple of hours to run on your systems (the really big databases will take much longer, but normally databases don't take very long to backup).  Because of this it is very important to ensure that the disks which the SQL Server will be backing up to are correctly aligned fox maximum performance.