I may be wrong here, but I think there's one good reason to use anything.example.com instead of example.com: with the naked domain, you can't have a separate domain for static assets which the client doesn't send the cookie to (for performance improvement). If you set a cookie with the domain example.com, it will still get sent to static.example.com.
Granted, you could use examplecdn.com or something, but then you have to register and manage more domains.
Yes, it gets propogated to subdomains, but the point was that if you have subdomain X.y.z, as long as you set the cookie for y.z, the cookie is valid for X.y.z and U.y.z.
My point was that you don't want the cookie to be sent to other subdomains, so you'd actually want to set the domain to X.y.z. You can't do that if you're web domain is y.z.
only reason www is usefull is because common cms (forums, blogs, comments, ....) convert www.example.com to a clickable link, but example.com not. yeah stupidbutthats the way it is.....