There will soon be an easy way to click and generally deal with JavaScript Dialogs with Watir (Web Application Testing in Ruby, pronounced "WATER"). It's always been possible, but the team is working on ways to make it easier. Until that day comes, we use the old way. Mark Cain posted sample code recently on the Wtr-General Mailing List. I'd been meaning to post my code that fires up another Ruby "thread," but his is arguably simpler if not slightly brute force. Thanks Mark!

#Put this method in your script:

def startClicker( button , waitTime = 3)
   w = WinClicker.new
   longName = $ie.dir.gsub("/" , "\\" )
   shortName = w.getShortFileName(longName)
   c = "start ruby #{shortName}\\watir\\clickJSDialog.rb #{button} #{waitTime} "
   puts "Starting #{c}"
   w.winsystem(c)
   w=nil
 end

#Then call it right before you click the button (or whatever) that
causes the javascript popup to display:

startClicker("OK" , 3)
$ie.button("Submit").click