Man I had to create an account just to comment on this.
(Interestingly I frequent a forum run by one of the writers, but he's not letting anything slip as to what they have planned, or any of the secret backstory. Did you know one of the guys who did the script for Psychonauts co-wrote the script for Portal? Anywho.)
The thing to remember about GLaDOS is that she's composed of "modules", which all sort of interact with and occasionally override each other. In the last battle you'll notice there's a "morality sphere", a "curiosity sphere", an "anger sphere", etc. And then at the end we find an entire *warehouse* of apparently still-active spheres.
So my take on what happened/is going to happen is this:
GLaDOS is at least indirectly responsible for the death of everyone at Aperture Labs - I believe she locked down the complex for security during the 7 Hour War in which the Combine took over Earth, but neglected to make any provision to keep the trapped employees alive, and at some point started storing up survivors in the freezer to use as test subjects. She then dedicated all her energies to development of the Portal gun, the project for which she was built.
I think that the poster above is onto something when he says that the test wasn't just for the Portal gun, but also a test of Chell herself - to see if she would stand a chance in the outside world against whatever's out there. However, given GLaDOS' schizoid character, I think even GLaDOS wasn't fully aware that that's what she was trying to do - rather, some module or another got a sense of higher purpose, and exploited or created blind spots in the other modules to redirect the test from simple tech demo to high-speed boot camp. So in a sense things are being planned out, but by an entity that has limited control within a larger, conflicted psyche that ALSO wants to "do science", protect itself, kill Chell, etc. In fact, the only way that entity could make this happen is by disguising its intent as an essential part of GLaDOS' prime directive - to complete research on the Portal gun.
I also think the previous test subjects, whether they were other employees or employee daughters or even clones of Chell, all failed, went insane, and died somewhere in the test complex. Chell is the first escapee, the first successful test. As far as cleaning up the bodies, considering the mobile floors and seemingly go-anywhere robot arms (like the one that snuffs out the candle at the end) I don't think that presents much of a problem.