We were using the great Isotope responsive layout jQuery plugin on a client project and found that because of the absolute positioning of divs there was an overspill when the isotope elements moved. If these items were relatively placed on the page obviously that wouldn't be the case. Our solution to this was to create a jQuery plugin/snippet to find the height of the isotope element and then nicely slide down the content area of the page. Here is the script:-
In our example, the isotope parent has the class 'clickable' and as we are using WordPress we are dynamically resizing the '.entry-content' parent div that contains the isotope divs. So for your own use simply identify the parent div/ul of the child elements that you want to calculate the height on and replace '.clickable' and then identify the content area (which in itself would typically be the parent of the prior) and replace '.entry-content' with the appropriate id or class.