I want to be able to click anywhere inside the body except that one specific element. I can\'t find out what\'s wrong with the code I have done.
When I click on the one
You don't really need any flags to do this. Just listen on body click and do different thing depending on the item clicked (event.target). This code should do exactly what you wanted (based on your code):
var body = document.getElementById('wrapper');
var except = document.getElementById('except');
if(body.addEventListener)
body.addEventListener("click", bodyClick, false);
else
body.attachEvent("onclick", bodyClick);
function bodyClick(event){
if(event.target != except)
except.style.display = "none";
}