One thing not mentioned was the excessive use of fixed elements that would have probably been rendered as frames back in 1999. They're not exactly the same, but most of the usage for fixed elements is replicating what a designer or developer would have used frames for, such as affixing a menu to stick to a certain area of the page no matter where the user scrolls.

Edit: Also modal popup windows everywhere, even where they aren't really needed (Twitter and the Chrome Extension Web Store are 2 that are questionable) instead of those js popup windows we used to see as browsers tend to block those. Maybe it's just me, but when you get to the point of having to put an entire page's content into a modal window, maybe it should be a separate page.