I've been having the same problem! However, I don't think it is actually a problem, more a change in design.
The rattling is caused by the mute button, when in the silent position. It should be less noticeable when in the 'normal' position. The button has apparently been made more flexible on the new 3G S models to reduce the risk of it breaking/straining under repeated use. I believe damaged buttons were quite common on the 3G?
Having seen this explanation on several sites, including the support section on apple.com I'm no longer concerned about my iPhones' little rattle 🙂