If it is Google Voice that you are getting the MWI (message waiting indicator) then going to your GV web page and marking all your voicemail and SMS messages as read should clear that indicator, although it may take some time. I have noticed it clear within a few minutes and other times it took a half hour or more. With GV I get the MWI on my phone when there are either unread voicemail or SMSes. I don't think there is a way to mark GV messages as read by dialing into your GV account, I believe the only way currently to clear them is with your GV web page.
Dave