It's not terribly flashy, but what about something like http://www.akamai.com/html/technology/dataviz3.html ?

Given the current state of this technology (requiring a STM and very low temperatures) I question how soon, if ever, this type of "computer" will become useful for independent nano bots, especially within the human body or other non-ideal environment. However, for working on a molecular scale to control things in a lab, this technology seems to have more immediate promise.