window.onload = function(){

	var allowUnload = true;
	
	window.onbeforeunload = function(e){
		//allowUnload will allow us to see if user recently clicked something if so we wont allow the beforeunload.
		if(allowUnload){
			//message to be returned to the popup box.
			var message = 'Are you sure you want to leave this page message',
				e = e||window.event;
			if(e)
				e.returnValue=message; // IE
			return message; // Safari
		}
	};
	// We need this to allow us to see if user has clicked anywhere if user has clicked we wont allow beforeunload to run.
	document.getElementsByTagName('body')[0].onclick = function(){
		allowUnload = false;
		//setTimeout so we can reset allowUnload incase user didn't leave the page but randomly clicked.
		setTimeout(function(){ allowUnload = true; },100);
	};
};

window.onload = function(){

var allowUnload = true;
	
	window.onbeforeunload = function(e){
		//allowUnload will allow us to see if user recently clicked something if so we wont allow the beforeunload.
		if(allowUnload){
			//message to be returned to the popup box.
			var message = 'Are you sure you want to leave this page message',
				e = e||window.event;
			if(e)
				e.returnValue=message; // IE
			return message; // Safari
		}
	};
	// We need this to allow us to see if user has clicked anywhere if user has clicked we wont allow beforeunload to run.
	document.getElementsByTagName('body')[0].onclick = function(){
		allowUnload = false;
		//setTimeout so we can reset allowUnload incase user didn't leave the page but randomly clicked.
		setTimeout(function(){ allowUnload = true; },100);
	};
};

var allowUnload = true;

window.onbeforeunload = function(e){
	if(allowUnload){
		var message = 'Are you sure you want to leave this page message',
			e = e||window.event;
		if(e)
			e.returnValue=message;
		return message;
	}
};

window.onclick = function(){
	allowUnload = false;
	setTimeout(function(){ allowUnload = true; },100);
};

I needed a method to confirm unload of the site, but still allow the user to click around the site this was my method of doing so.

Confirm leaving your site onbeforeunload

JavaScript