[jquery] Change Active Menu Item on Page Scroll?

Just to complement @Marcus Ekwall 's answer. Doing like this will get only anchor links. And you aren't going to have problems if you have a mix of anchor links and regular ones.

jQuery(document).ready(function(jQuery) {            
            var topMenu = jQuery("#top-menu"),
                offset = 40,
                topMenuHeight = topMenu.outerHeight()+offset,
                // All list items
                menuItems =  topMenu.find('a[href*="#"]'),
                // Anchors corresponding to menu items
                scrollItems = menuItems.map(function(){
                  var href = jQuery(this).attr("href"),
                  id = href.substring(href.indexOf('#')),
                  item = jQuery(id);
                  //console.log(item)
                  if (item.length) { return item; }
                });

            // so we can get a fancy scroll animation
            menuItems.click(function(e){
              var href = jQuery(this).attr("href"),
                id = href.substring(href.indexOf('#'));
                  offsetTop = href === "#" ? 0 : jQuery(id).offset().top-topMenuHeight+1;
              jQuery('html, body').stop().animate({ 
                  scrollTop: offsetTop
              }, 300);
              e.preventDefault();
            });

            // Bind to scroll
            jQuery(window).scroll(function(){
               // Get container scroll position
               var fromTop = jQuery(this).scrollTop()+topMenuHeight;

               // Get id of current scroll item
               var cur = scrollItems.map(function(){
                 if (jQuery(this).offset().top < fromTop)
                   return this;
               });

               // Get the id of the current element
               cur = cur[cur.length-1];
               var id = cur && cur.length ? cur[0].id : "";               

               menuItems.parent().removeClass("active");
               if(id){
                    menuItems.parent().end().filter("[href*='#"+id+"']").parent().addClass("active");
               }

            })
        })

Basically i replaced

menuItems = topMenu.find("a"),

by

menuItems =  topMenu.find('a[href*="#"]'),

To match all links with anchor somewhere, and changed all that what was necessary to make it work with this

See it in action on jsfiddle