Portal 2, writer Erik Wolpaw said during the Plot vs. Play panel (co-hosted by Joystiq's Ben Gilbert) at PAX Prime today.
Wolpaw described the following scene, which was cut from the final version of Portal 2 after Valve realized it was too vague mechanically for players to enjoy: Cave Johnson's voice said, "I'm Cave Johnson" over the intercom, followed by, "No, really, I'm Cave Johnson. Look down." Cave's personality was trapped in a computer and he begged to be unplugged, while players found use in his hardware and had to push him against a wall to jump on a ledge.
In the end, the gameplay didn't fly and the scene – and story arc featuring Cave in a computer – was removed entirely. We like to think that means Cave got his wish, and he's not still trapped inside a box, screaming about lemons and plugs.