In recent times, I and my colleagues at the Foresight Nanotech Institute have moved towards discouraging the idea of self-replicating machines as part of molecular nanotech. Eric Drexler, founder of the institute, described these machines in his seminal work "Engines of Creation," while also warning about the major dangers that could result from that approach.
Recently, dining with Ray Kurzweil on the release of his new book The Singularity Is Near : When Humans Transcend Biology, he expressed the concern that the move away from self-replicating assemblers was largely political, and they would still be needed as a defence against malevolent self-replicating nanopathogens.
I understand the cynicism here, because the political case is compelling. Self-replicators are frightening, especially to people who get their introduction to them via fiction like Michael Chrichton's "Prey." But in fact we were frightened of the risks from the start. Self replication is an obvious model to present, both when first thinking about nanomachines, and in showing the parallels between them and living cells, which are of course self-replicating nanomachines.
The movement away from them however, has solid engineering reasons behind it, as well as safety reasons. Life has not always picked the most efficient path to a result, just the one that is sufficient to outcompete the others. In fact, red blood cells are not self-replicating. Instead, the marrow contains the engines that make red blood cells and send them out into the body to do their simple job.