Types of danger
From Wise Nano
There are several kinds of dangerous products of molecular manufacturing (MM), and it's important to distinguish between them because they need different kinds of containment/control.
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Direct Harm
Products that can do direct harm to others (and, many would add, socially undesirable harm to oneself). MM could make very small weapons, so the harm from, say, a cubic meter of these products could be quite large. But it's limited.
A secondary grouping of technologies nanotech is likely to improve, perhaps to cause 'direct harm' to society, is surveillance. Being able to gather images from every 'n' meters of walkway, track people via pollen-sized devices, and/or use high-powered computer pattern recognition systems to detect 'aberration' or 'dangerous activities' would lead to a very effective screen against many threats - but could also be perceived as a deathblow to personal freedoms.
Unregulated Nanofactory
In an unregulated scenario, having a nanofactory that has no restrictions may make you safer--as long as it can't be remotely hacked, which it probably can. One in every house probably makes the neighborhood less safe, because it increases the chance that someone will hack or misuse one of them. People today are, to put it politely, uninformed enough to install obvious viruses on their own computer, even when they have to run them through a decompression program first. Someone who wanted to put spyware in a neighborhood would find it pretty easy to convince one in a hundred people to install it.
Black Market
Any restrictions on nanotech development has a potential to generate an illegal ('black') market, if there is enough market interest in the banned/restricted materials or capabilities. The very existance of such an option could be a dealbreaker for an otherwise worldwide defensive agreement on nanotechnology, leading to some of the more blatant physical destruction possibilities - or perhaps the surveillance/"scream" scenario, given certain preconditions.
The capabilities of nanotechnological sensing would theoretically make this quite a difficult enterprise - high risk of detection, followed by high risk of capture/destruction (depending on the organizational leanings of those that detect the activity, among other factors.) Yet missing only one self-replicating device would start the cycle of searching all over again, making this potentially a massive headache for law enforcement organization(s).
Small Free-range Replicators
Anything in this class would be quite hard to design. But not impossible. They wouldn't be useful as products or weapons, but would appeal to the kind of people who wrote the first computer viruses. By the time it becomes possible for individuals to design and build these, the situation likely will have developed far beyond today's planning horizon. And for dangerous-to-humans potential, non-replicating weapons are a more extreme and urgent threat.
Cumulative Harm
If everyone had a personal supersonic airplane, and there were no restriction on sonic booms, life could get pretty miserable. And there's nothing wrong with a square mile of solar cells in a desert, but a million square miles could change global climate. This kind of harm can be dealt with only by regulation, since there is no personal incentive to mitigate it, and there won't be enough natural scarcity to limit it.
Subversion
Imagine a device that takes software instructions and does something. Now imagine a piece of software that says it'll make product X, but really produces lots of product Y. With the advent of programmable nanofactories, no longer are these products limited to electronic representation, but may become physically present. Even more nefarious are those codes which promise product X, and produce product X, but add capabilities useful for the developer at the cost of the user. (The typical response to this danger is an accrediting authority and encryption. I expect this to work as well as it works in the software arena today.)
"Scream"
As per Dr Bostrom's Existential Risks paper, one of the major threats from such a technology as nanotech may be characterized as a 'scream'. That is, a small group uses high technology to supress the majority's technological options, and hence forms a totalitarian regime with very small chance of successful revolt/overthrow (save potentally from within). Note that nanotech could meet many of the other scenarios in Dr Bostrom's paper.
"Invisible Effects"
A concern sure to strike chords for those who promote the Precautionary Principle, nanotechnology may have "invisible effects" that are beyond most if not all humans' imagination. Some possible examples: Melting icecaps, destruction of the ozone layer. (Originally raised by Mike Treder from CRNano.org)
Risk to Intellectual Property
Full-blown nanotech has the capability of taking something apart at the atomic level, making records of how it was constructed, and then making as many new copies as desired. This has obvious challenges for guarding intellectual property or other such rights (branding, etc).
