MISSION CRITICAL (Legend Entertainment, commercial software for the PC) should be added to your list of computer games that reference nanotech.
This is a *great* adventure game in terms of both multimedia presentation and content/story/ideas. In the 22nd century, two human factions are fighting an interstellar war over the issue of whether or not unlimited technological progress should be permitted. (The anti-tech faction fears the emergence of superhuman AI.) It is up to the player, as the sole surviving crew member on a military-scientific mission to a distant planet believed to contain remnants of advanced alien technology, to complete the mission, thereby tipping the balance in favor of the pro-tech faction and the Singularity.