Pretty simple suggestion, I think: Have the option to merge referrals from websites that start (or don’t start with) www.*. Some sites strictly enforce www. on or off, but some work either way, and it can muck up the referral stats if you have 5 hits from site.com and 5 hits from www.site.com.
So my suggestion is to either automatically, or via an option, merge all site referrals from “site.com” and “www.site.com”.