I dropped off my '07 Yaris at the dealership today. I've had some clutch chatter in first gear when it's cold, and in reverse all the time; something other Yarisworld owners have also had. Let's hope the dealership has a fix, or that it's not a major issue.
My 2005 Scion xB also had some clutch issues, although they were totally different (slipping clutch, throw-out bearing). FYI, I have owned seven cars with manual transmissions, and never had any problems, sans my xB and Yaris. Let's hope it's just coincidence!