Bumping this thread now because it might as well serve it's intended purpose. Please keep spoilers in tags, as I know one or two others are playing or intending to play through the game ATM.
Well, took me long enough to get round to it, but that's me done. I changed my tack a little from my previous post after realising that unconscious people don't get up again, unlike in Hitman. Also I started to feel bad about killing people who probably didn't deserve it quite so much as those who were actively out to murder me, like security guards.
So I chose David Sarif's ending. Despite the fact that he lied to and manipulated me, his vision for the future still most closely matches my own. I think people should be free to push the boundaries of science and technology without restrictive regulation based on shaky, often purely hypothetical moral arguments. Leaving humanity's future in the hands of corporate types like Sarif might seem unnerving, but if someone were to ask me "Who is doing more good for the world, US lawmakers or Bill Gates?" then I'd choose Gates without hesitation. Obviously they are interested in making money, but leaders in the tech field still seem to have far more interest in improving lives and furthering humanity than high-ups in say, banking or the oil business... or even politicians.
I'm not sure it would have been the ending Jensen would have chosen - As well as being the most moderate, I get the feeling Taggart's ending is the most canon. His doesn't damage the reputation of augmentation but regulates it (you could see why Jensen would want this after he learns of his history) and furthers the agenda of the Illuminati, which would all tie in to the original game. Darrow's ending would expose the Illuminati and put the brakes on augmentation (which we know in DE1 didn't happen) and after all the trouble he's been to I doubt Jensen would just go "f*ck it" and press the Big Red Button either (and what would be the point of destroying the Hyron Project to stop the signal that was sending the augmented people in Panchaea mad if you were ultimately going to kill them all anyway?)
All things considered I found HR a very enjoyable game, and certainly worthy of the Deus Ex name. On to The Missing Link!