The blindingly obvious..
Not sure why this has only just struck me but it has. If you are designing databases, storage groups etc.. why not place all mailboxes that belong to the same department across the same set of databases. In theory this will improve your single instance ratio as emails to the entire department for example are likely to be stored in fewer databases....
And of course the more efficient your SIS is then the more you reduce your IOPS to the disks.
(Use performance monitor and the 'single instance ratio' counter to work out how effective single instance storage is across your Exchange Servers.)