// Create a Skype4COM object:
var oSkype = new ActiveXObject("Skype4COM.Skype");

// Query the total number of missed messages:
WScript.Echo("Total missed message count: " + oSkype.MissedMessages.Count);

// Query the id, timestamp, and sender Skypename of the message:
for (var i=0; i < oSkype.MissedMessages.Count; i++) 
{
  var oMsg = oSkype.MissedMessages.Item(i+1);
  WScript.Echo("Msg id: " + oMsg.Id + " at " + oMsg.Timestamp + " from " + oMsg.FromHandle);
}
// Mark the missed message as "Read"
for (var i=0; i < oSkype.MissedMessages.Count; i++) 
{
  var oMsg = oSkype.MissedMessages.Item(i+1);
  oMsg.Seen = true;
}