First of all, I have to warn you that this article contains spoilers. Major, game-destroying spoilers. If you haven't finished Portal 2 yet, you'll probably want to skip this entire article until you've finished the game. Don't worry, you can always come back later.
I'm a bit tired of all these Portal 2 rumors spreading around that Caroline is GLaDOS. She's not. You want to hear my logic on this?
First of all, here is the portion of the game this rumor comes from. Cave says: "Brain Mapping. Artificial Intelligence. We should have been working on this thirty years ago. I will say this – and I'm gonna say it on tape so everybody hears it a hundred times a day: If I die before you people can pour me into a computer, I want Caroline to run this place."
Cave is planning on preserving his own brainwaves on a disc so that he can continue to run Aperture Science after his death. If that doesn't work, he wants Caroline to run the place. He even gives permission to his engineers to insert her into his computer against her will. According to my interpretation of all this, Cave was successful and it was not necessary to have Caroline run the place.
Now, let's look at the evidence. In the ending of Portal 2, GLaDOS has a moment of compassion for Chell. She blames this on Caroline, who lives in her brain. After a message stating: "Caroline deleted," GLaDOS goes back to her original self. Caroline was the personality that was keeping GLaDOS restrained during the second half of the game.
And here are some lines from the end credits song (sung by GLaDOS to Chell):
"She was a lot like you / (Maybe not quite as heavy) / Now little Caroline is in here too."
This obviously means that Caroline was a personality core that was inserted into GLaDOS; she's not GLaDOS. Caroline (as a human) was a lot like Chell, only not as heavy. If you've played through the game, you'll remember GLaDOS' jokes about how Chell has gained weight. GLaDOS even blames a faulty Arial Faith Plate on her heaviness. Later in the song we have these lines:
"Goodbye my only friend / Oh, did you think I meant you? / That would be funny if it weren't so sad."
"My only friend" is Caroline. Not Chell. GLaDOS clearly states that Chell is not her friend. The song goes on:
"Well you have been replaced / I don't need anyone now / when I delete you maybe I'll stop feeling so bad."
This in an obvious reference to the part of the game where GLaDOS deletes Caroline. It's an ironic statement, because GLaDOS won't feel bad about deleting her conscience once her conscience has been deleted. So the few lines GLaDOS sings about Caroline all refer to her as something other than GLaDOS or Chell.
So who is GLaDOS? Well, here's an interesting theory that may sound a bit farfetched at first, yet is painfully obvious after playing through the campaign a few times. GLaDOS is Cave Johnson.
"But Cave Johnson is a man and GLaDOS is obviously female!" you exclaim. But you're wrong. GLaDOS is an AI. GLaDOS has no real gender. She (yes, I will continue to refer to GLaDOS as "she" because we're all so used to it) has some female qualities, including the artificial, auto-tuned feminine voice, but that doesn't mean she is actually female. And is it too implausible to imagine a male personality inserted into an AI that has female characteristics?
Once you get over the whole "female" thing, the rest of the pieces fall into place very quickly. GLaDOS and Cave have incredibly similar personalities. Both are power hungry, are highly intelligent, will go to great lengths to "do science," and have been known to kill people (and cats) in the testing process. Cave even admits to inserting tumors into test subjects and converting their blood to pure gasoline without their consent. Those sound an awful lot like things GLaDOS would do.