It looks like they're adding an "onclick" event to links, which stores the recent history in the "<username>_recentclicks2" cookie as '%' delimited story IDs.
If you add an "onclick" event to a link it will fire before the browser changes the page, in the same way an "onsubmit" will fire before a FORM submits.
<a href="http://google.com" onclick="alert('You clicked me. Now redirecting you!');">Click me</a>
The same is true of click events that you bind using jQuery.