One of the implications of molecular manufacturing is major advances in avionics. Materials 100 times as strong, motors and computers a million times lighter, and seamless, automated, rapid construction, will enable rapid R&D of highly advanced aerospace systems. Advanced aerospace systems could be used for easier space access (including rapid testing of advanced propulsion concepts), delivery of sensor platforms or weapons, personal transportation, and a number of other beneficial and scary applications. Unmanned aerial vehicles (UAVs) will become far more capable.
We can get a sneak preview of some of the concerns in a recent article at PhysOrg.com: "Flying robot attack 'unstoppable': experts" which describes some of the technologies that are already available, some of the ways they are being used, and some fears about the ways they might be used in the future. "The technology for remote-controlled light aircraft is now highly advanced, widely available -- and, experts say, virtually unstoppable." Small planes don't show up on radar. They can carry hundreds of pounds of payload. They can be guided by GPS. They have already been used by paramilitary and terrorist groups. The concern is that they could deliver explosives to a target with near-pinpoint accuracy.
The article doesn't mention it, but UAV technology is becoming available to hobbyists, and not only for sinister purposes. A group at MIT is building the "Freedom Flies family of UAV's" which can carry fifteen pounds of "video, gps units, pamphlets, water, food and other payloads." It is intended to cost a few thousand dollars, and to be open source (plans freely available). They admit they are still crashing quite often, but that will presumably change soon.
It remains to be seen whether private UAV development will be viewed with as much suspicion as, say, hobbyists blowing up junk for their own amusement (they tend to get called "militias" and prosecuted). There is certainly a contrast, even a tension, between the two websites linked above. A major positive use of UAVs might be to increase accountability by photo-documenting abuses that governments and corporations would prefer to keep hidden. However, from the point of view of those being watched, this is indistinguishable from spying. The article on terrorist uses did not talk about this, but it may turn out to be the biggest issue raised by UAVs.
UAVs are one tiny sub-category of one implication of molecular manufacturing. Even pre-MM technology is cause for concern, and capabilities are already coming online and becoming widely available to individuls and small groups. General-purpose molecular manufacturing will enable hundreds of equally significant advances--many of which no one has thought of yet.
Today's development of UAVs will give the world a chance to get used to at least one kind of robot that can go almost anywhere (that's not too small) and carry out actions remotely. This is probably a good thing. But it also means that software for UAVs will be pretty well understood by the time MM arrives.
The world is going to be a very interesting place.