Read the book "Bicycling Science" (really great book by the way!!!) for some hard data on chain drive efficiency with various setups. Long story short, a dirt-drive derailer-geared system with a clean chain is about 98-99% efficient with a cog of 15T or larger. An internally-geared system is around 5-20% less efficient in non-direct drive, depending on its construction. And chain cleanliness is fairly irrelevant, since it will affect derailer- or internally-geared bikes nearly equally, given that they both use a chain going from a chainring to a cog.

Internally geared hubs are quite expensive: today's equivalent of the 3-speed Sturmey-Archer would probably be the 7-speed Shimano Nexus hub, which I couldn't find for < $150. By contrast, I can get a pair of Shimano LX or Shimano 105 derailers, rear hub, and a 9-speed cassette for about $100 from Nashbar. The LX setup will have a slightly wider and more finely spaced gear range, and is quite a bit lighter. The difference *may* be due to economies of scale in large part, but I'm not sure...