Hurrah! The laser cut acrylic for my NIXIE tube clock casearrived this morning, and amazingly all the parts fit together nicely. The screw holes even matched up with the PCBs!
I'm pretty happy with how this turned out, and I can finally say the nixie clock project is finished. I definitely learned a lot for the next clock - like use the RTC with an onboard crystal! I'm thinking of perhaps making a wordclock.
You can check out the Inkscape files I sent to Ponoko for manufacture here (they are released under CC BY-SA 3.0 if you are interested).
In unrelated news, design on revision four of my motor controller is nearing completion, so hopefully the thing will be flying soon!