Add page animations prior to following a link. Here it is setup for the main navigation, using GSAP for animation.

gistfile1.txt

function closePage(href) {
              var pageSwitching = new TimelineMax({ paused: true});
              pageSwitching.insert(TweenLite.to($('#contentShell'), 1.25, {css:{ autoAlpha: 0, top: 1400 }, ease: Expo.easeInOut}), .1);
              pageSwitching.insert(TweenLite.to('#top_bg', 1, {css:{autoAlpha:0, top:-900}, ease: Expo.easeInOut}), 0.15);
           
                      
              pageSwitching.play();
              
	      setTimeout(function() {
			
                        gotoPage(href);
                        
		}, 750);	
}


function initButtons() {
              $('#main_menu a').click(function(){
                            var href = this.href;
                         
                            if ($(this).attr('target') == '_blank') {
              			gotoPage();
                            }  else {
                            	closePage(href);
                            }     
                            return false;
              });
}
function gotoPage(href){
	window.location = href;
}
initButtons();