I think the Bayer filter has still got some legs left. I think a possible candidate to replace it is the reverse of what they do with those one laptop per child computer screens (edit: actually, now that I read this it looks like they went away from the prisms, but they still have the image that shows the concept—the first one on the right if you look at that link). They use a prism to split up the light into its color components just before it goes through the pixels of the screen, and the lack of a color filter lets you pass almost all the light, instead of throwing light away by absorbing it in a color filter like a standard display. Someday I'll bet they'll have microprisms that do something similar on imaging sensors—split the light before it hits three separate photodiodes for each pixel. Or maybe they could have more than three channels(?). I think it would be fun having channels for near-IR, red, orange/yellow, green, blue, and violet. You could save an image based only on the IR channel, for example.
While we're on the subject of the bayer filter, what do you guys think about a camera with a modified sensor (maybe DX to keep it inexpensive) that has no bayer filter and no AA filter to shoot black and white only? If you did this to the D300s sensor, it would give you a camera with a base ISO of around 800 with noise there comparable to the D300s at ISO 200, but it would buy you around two stops on the high-gain end, as well (compared with acceptable noise at ISO 3200 on the bayer pattern sensor, you would have acceptable noise at ISO 12800 on the non-bayer sensor). I know it's a niche market, but I'm sure a few people would buy them and it doesn't seem like it would be too hard to implement.