Why not CFLs? Fluorescent lighting is totally inappropriate for photographic devices like these. First of all, fluorescent lights flicker at 60 or 120hz. Flicker isn't their only problem, they actually actively change color as they flicker. That means that if you get the luminance up high enough to use a fast shutter speed and a small aperture (remember our perfect world), you will have problems where the colors and illumination will appear different on different photographs. To illustrate this, I took a high-speed video of a flourescent light flickering. I think it speaks for itself.
Update: I have had several comments that this video is misleading. There is a discussion about this in the comments. The primary point of argument is that most, if not all, CFL (the small, socketed fluorescents) flicker in the KHz instead of Hz. This is true. However, even if flicker is a non issue, they are not as bright as halogens, which, multiplied times the need for more bulbs (because they are not as bright) just saps the nice green construction of this project with a bunch of mercury.
There are other, more technical reasons to prefer bulbs with a more continuous spectrum, but for that, please read the comments. /Update
LED lighting is cool, but it is not very high intensity unless you use high power LEDs, like Luxeons, Crees, or SSC P7s. And the problem there is that these LEDs are very expensive, and require heatsinking and driver circuitry. And you have to ship them over from China to get good prices! Not very green. And there are color issues. LEDs, even LEDs from the same "bin" (meaning they have similar performance characteristics) can have very different colors. While evaluating light sources for this scanner, I bought two identical 3-watt LED flashlights from Target. They use Cree LEDs, and here is a picture of how different their color rendition is. Far from ideal. Also, many LED flashlights flicker, too.