It's a mini prototyping area, like what you get with a separate prototyping shield but directly integrated into the main board. You can use it to add parts to the Eleven that you want to be permanently connected, like if you're building the board into a project and want to make it low profile.
John Boxall from TronixLabs / TronixStuff has a great article here showing how he used it to put an RTC on an Eleven:
http://tronixstuff.com/2010/10/07/add-a ... twentyten/
I've tried to fit some prototyping space on our Arduino compatible boards whereever possible. Even the EtherMega has a small spot that doesn't look like it would be big enough to be useful, but I've used that myself a few times. On the old EtherMega I used to install a MAC address chip in that space, but in the current EtherMega I incorporated the MAC chip straight into the design. I've also used it to put a watchdog timer on the board.