In my opinion, security is the biggest benefit.
Suppose you purchase software from a company that uses a SQL database. Also suppose that this software requires system administrator priveleges. Obviously, this wouldn't be the best way to write the software, but just suppose it existed.
Now, you wouldn't necessarily want this software to have access to other data that you may be storing in your system, so, you could create a named instance and give them system administrator priveleges to that instance.
-George
Strong and bitter words indicate a weak cause. - Fortune cookie wisdom