This example uses jquery-cookie
Check if the cookie exists and has not expired - if either of those fails, then show the popup and set the cookie (Semi pseudo code):
if($.cookie('popup') != 'seen'){
$.cookie('popup', 'seen', { expires: 365, path: '/' }); // Set it to last a year, for example.
$j("#popup").delay(2000).fadeIn();
$j('#popup-close').click(function(e) // You are clicking the close button
{
$j('#popup').fadeOut(); // Now the pop up is hiden.
});
$j('#popup').click(function(e)
{
$j('#popup').fadeOut();
});
};