Josiah H. has another great clock that he made - a blue-phosphor neon lamp based binary clock. It is a 6 by 4 display of neon tubes that are directly driven to avoid dimming due to multiplexing. The design is based on the ATmega328 and we developed on an arduino. He event was as far as writing all of the software himself including the clock/timekeeping arduino libraries that are available. As far as driving the displays go, a 24 bit shift register drives a series of MPSA42 NPN transistors to actually drive the displays.
As usual, he has a great writeup on his site.