Good question but there are many answers depending on many things like users, use of system, network and such. In general I would do the obvious on SQL and put database files on different disks, enough RAM and keep indexes maintained. When this is not enough I would focus on some focused changes in the Navision application depending on what problem you have.
Navision is a most often used as FAT client (2009 has thin client) where network connection to server and harddisk speed on server is most important.