I ultimately came up with a couple of ideas in this regard; one seemed potentially doable, and the other seemed absolutely doable. Both rely on the idea of the main building material being plywood or OSB - like 1/2 - 3/4 inch thick 4x8 sheets (or the metric equivalent).
The first concept was something that a "do-it-yourselfer" could own or rent. Essentially it was to be a plotter you would attach (in some manner) to the sheet of plywood, and it would "plot" the outlines of the cuts and such on the wood (at the time, I envisioned an ink-jet like approach - today a small LED laser engraver might work better), with annotations and other such things to guide the builder in fabrication and assembly. These annotations could also refer to areas in a reference assembly diagram or software that could take the user step-by-step in cutting out the pieces (using various tools - a jigsaw and circular saw mainly) and assembling them (perhaps with 3D views, audio, graphics, etc). The plywood pieces would also be numbered or otherwise noted so that each is used in the proper order. The whole thing could be sold as a simple robot, perhaps attached with cords or something to the wood, in a case with software - user supplies a laptop (or perhaps it comes with it?).
This machine actually does exist - in a way nowadays. I know of a CNC router that attaches directly to a piece of plywood, which could cut the parts directly; however they wouldn't be numbered (but perhaps they could be engraved?). There's also another tool that is something like a "user guided" CNC router; the user holds the tool, and guides it based on an on-board reference (I'm not sure, but I think it can also help to auto-correct problems). Ultimately, both of these machines come really close to the first concept I had. It's nice to know someone had the same ideas and took it further - but that's to be expected, I guess.
The second concept I had was something that I could only see as either an owned piece of equipment, or as a rental/lease system. Essentially, this would be a container (ideally a standard shipping container). One end, you'd load an "elevator" of plywood sheets (like a printer of sorts), the pieces would go inside the "magic box", and would be spit out the other end (again, stacked) as mostly pre-cut pieces of plywood containing the parts of the building.
Think of these pieces as being similar in scope as those "pop-out" wood puzzles of dinosaurs and such you can buy as toys, just larger scale. The cuts made by the machine wouldn't be "complete", but would have to be completed by the user using a jigsaw or handsaw. This would also allow shipping pre-cut pieces (which could be made in a factory) to a building site. Perhaps these could be "ordered online". But the original concept was that the container box would be dropped off at the on-site building location, with a load of "blank" pieces of plywood/OSB.
Inside the box would be a simple system of conveyors and other plywood material handling devices that would move the pieces from the input stack, to a cutting machine, then to the output stack. The cutting machine could be either a CNC router (like a 4x8 shopbot or similar) or some kind of large (2-300 watt?) laser cutter. The latter might be preferable, because it could also engrave assembly annotations, etc on the parts.
The downside of this machine (actually both ideas have similar downsides) would be the fact that you'd need to monitor and do tool bit changes as they wear - or in the case of a laser cutter/engraver - monitor and prevent fires from starting. Which would seem to make this kind of a system more suited to a "factory floor" installation rather than an on-site system rented by a diy'er or a contracted builder. Then you'd just go online, select a floorplan/style, make certain mods as available, and order. Completed sheets of the parts would be delivered to your building site (perhaps with all needed fasteners and such).
Lastly - I'd be willing to bet that such a system (and the "WikiHouse" designs) - at least in the United States - will suffer from the same issues that plague people who want to use other alternative construction techniques (aka - rammed earth, straw bales, earthship, etc): That of the hassle of getting permits approved for the construction, then obtaining homeowners insurance for the resulting structure. In some areas, both can be so onerous as to make such construction impractical, more expensive, or impossible...