I think part of the reason they stopped making them was that there is no way you could put one of the newer G4 processors in there. The faster they run, the more heat they kick out - when they made the cubes, G4s ran at, what was it, about 400 MHz? The heatsink that was needed to keep them cool (in a mini-tower) was pretty small, so they could get away with making the heatsink a bit bigger and taking out the fan.
Have you seen the size of the heatsink they have to put on the 800 MHz G4s? And that is with a fan running over the cards & processor, and another fan drawing power out over the power supply. The heatsink is almost as big as the whole Cube was. Take the fans out of the thing, and you'd have a puddle of melted transparent plastic pretty quick - that or they could go back to releasing 400 MHz G4s.
I wouldn't mind the slower CPU so much, I hate that the only fanless Mac now is the iMac...