What if the simulated people that Neo blithely shot in the Matrix were actually self-concious?
I think in the first movie it mentions that they were definitely people, not programs, but because the Agent programs could SSH into normal people whenever it deemed necessary, they all became a liability for the goal of liberating the greater majority of people. Unless you meant the Agents as a program, and not their hosts; in which case, perhaps one might log the output of top as the "killall -9 top" command is run.
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ERROR: It hurts, steve....so...dark
That said, I wonder what pain is felt or maintained by something that is virtually immortal.
There's also a pretty rich tradition of epistemology prevalent in mythological thought. The universe, according to Hindu beliefs, for instance, is nothing more than the dream of the creator deity Vishnu ("Life is but a dream"), in addition to the quasi-schizophrenic idea of Maya (the veil of illusion; all reality is illusion, etc.). Joseph Campbell's books (ie, Hero With a Thousand Faces) touch on some obscure dimensions of all that, and connects it to similar systems of mythological thought.
Unrelated: I dreamed last night that one of my colleagues (not in the computer science/engineering/software fields) recompiled the linux kernel with all the grsec features with no negative repercussions against any programs or GUI features. I think I need to spend a few days camping...