With my limited (read "non-existent") crafting resources (e.g. space, tools), the easiest way to enclose my Arduinix clock was by recycling my late Chumby's shell. Things almost magically fit together, with minimal thinking and work. I was able to cram inside the box a hand-wired Wiseduino with an Arduinix-remix shield and a 4-tube board.
The old Wiseduino would have come in handy if I had any left. I made one using the protoshield from Sparkfun, which also has a connector for the Bluetooth JY-MCU module. Beside the ATmega328, this pseudo-Wiseduino board includes a DS1307 with coin backup battery and a 7805 voltage regulator.
The tube board is attached with screws to an empty board that plugs in the Arduinix-remixed shield. (Note that one reason for "remixing" Arduinix was to re-arrange the parts sticking out, namely the mosfet and the capacitors, so that it allows another shield to be stacked on top.)
The clock has no user button (I glued the original snooze button on top, would have required extra work to re-use it), so the time is set through the bluetooth interface, similarly to my other Arduino Nixie clock.
The sketch (compiled with Arduino 1.0.4) is available here. Note that, unlike the original Arduinix sample sketch, the nixie-driving code is now using interrupts. This decouples the display logic from the clock functionality, also allowing for the addition of a buzzer alarm.