http://www.withurwe.com/ was quite interesting, and I think it was mentioned on mises.org already.
I can’t say much about the others, but you completely misinterpreted Deus Ex.
Yes, the ultimate bad guys are businessmen. but they aren’t bad for being businessmen, they are bad for using the government for the sake of dominating the world. Also, they aren’t bad for not giving nanotechnology to the “people”, either. It is expressly stated that the cost of making a person’s immune system compatible with nanites is tens of billions of dollars, and those introduced to the (otherwise beneficial) nanites get the Gray Death, resulting in, well, death. However, they ARE evil for introducing the Gray Death so as to cause enough unrest to justify taking over.
Also, most of your allies are distinctly libertarian in nature. You have the NSF (rebels who rose up because the US government suspended the 2nd Amendment), Tracer Tong, and Silhouette. The Illuminati aren’t so great, but it is pretty clear that they are just a slightly less tech-savvy and more benevolent version of MJ12.
I went with the Dark Age ending. Destroying the base is clearly the best thing to do, as it means people can redevelop technologies without MJ12 taking control of them (as they did using the Aquinas Protocol with the Internet). Admittedly it has its problems, but it beats being controlled by a dictator or the Illuminati (those guys seem very out of touch with reality, and they would doubtless cock things up if they were in charge).