StackOverflow - When clicking a tab in the help bar, the matching icon on top of it start jumping up and down.
/video - http://d.pr/wtEd
iOS - When you enable airplane mode on iPhone, a little airplane icon flies from the edge of the screen.
Chrome - Status bar shift down with the cursor when it is hovering a link near the bottom of the page. After a few seconds its hows the entire URL.
Apple - Menu drops down and bounces a little bit. Search bar expands intelligently once activated and shows different search results depending on what page you are on.
/Thanks to Renato for being the first to submit.
New Scientist - Simple optical illusions can make it seem like the progress bars on your file downloads are moving faster than they actually are.