Profile Boxes are the third-party applications that are featured in boxes on your profile. You can now add a “bookmark” to the left side of the Facebook home page for these applications.
What will happen to my Boxes in the future?
As part of our ongoing efforts to improve the user experience and promote consistency across the site, soon Facebook will no longer support profile boxes from applications. In order to access your favorite applications more easily, you can bookmark them.
To learn more you can visit the help page on this topic. Like I said, this really doesn’t matter much to me, but I know many other people with a lot of these such boxes that will now be going away.