The Clone, The Cube and the Construct by game-ism, parts 1 and 2. You'l have to find part 3 on your own.
http://www.game-ism.com/2008/04/13/the-clone-the-cube-and-the-construct-part-1/
http://www.game-ism.com/2008/04/14/the-clone-the-cube-and-the-construct-part-2/

That's part of what makes Portal almost unique. Like Ico and Shadow of the Colossus the player gets to decide on the story. Sure, you can say it's just the standard sadistically insane AI, but where's the fun in that?

Working backward from the empty world Chell finds topside, GlaDOS is trying to train a Chell to survive outside, learning from trial and error. That has led to torturous and frequently fatal treatment of Chell as the most effective training method. This approach has driven GlaDOS insane, because the prime imperative is for Chell to survive.

GlaDOS was training someone who could survive in the current conditions outside. Given the ad hoc nature of the training and the need to use clone androids this seems to mean each previous speciman failed when released to the outside. So GlaDOS has been ramping up the difficulty, and adapting her own interactions with each Chell to find the combination that maximizes survival potential.

Think about that. GlaDOS may have started out friendly and encouraging, but found that just didn't work well enough. GlaDOS has 'raised' and nurtured Chell after Chell, losing all of them. Either on the course or they left and never came back. Her own desires for Chell to succeed have forced GlaDOS to act cruel and sadistic, torturing Chell in the name of survival.

What really clicked was GlaDOS saying that the Weighted Companion Cube would never want to be a burden to Chell. The Companion Cube may have started as a psychological device to help Chell, but GlaDOS is projecting her own feelings onto it as well.

This really fits with Game-ism's theory that GlaDOS is raising this version of Chell to kill her. GlaDOS has had enough of torture as 'tough love.' Maybe the results of previous runs have pointed to the willingness to kill to survive. Just because they didn't survive long term doesn't mean previous Chell's didn't report back as much as possible, but they were too dependent on GlaDOS to survive on their own.

Which is not so say GlaDOS approach would work universally. It's possible Chell is being cloned over and over again, with upgrades, as a control. Like the movie Paycheck, this scenario is being heavily customized to a very specific scenario.

Finally, "This isn't brave, it's murder. What did I ever do to you? You don't even care, do you?"

The first sentence describes GlaDOS training sessions as much as Chell's impending act. The second sentence highlights the ambiguity of the training. Intended to train, it also kills. But GlaDOS has no choice if Chell's ultimate survival is in question. The last sentence is the cry of a rejected mother. A mother rejected in this case by a child specifically trained to do so.

Yes, all of this can be discarded as nonsense. The standard 'Artificial Insanity' scenario fits well enough. It's just interesting that Portal leaves enough clues to point to a different, much deeper, story.