A very quick crude demonstration of Binary Code Modulation for Angus Gratton which I did on the way home from OpenLab. I haven't tested this, so no guarantees.

globals.h

#ifndef GLOBALS_H
#define GLOBALS_H

#include <Arduino.h>
#include "nixie.h"

#define LATCH_PIN  8
#define CLOCK_PIN  12
#define DATA_PIN   11

#define DELAY      2
// max number of nixie tubes
#define MAX_TUBES   6

extern volatile byte bit;
extern volatile Nixie tubes[];

#endif

nixie.cpp

#include "nixie.h"
#include "globals.h"

// Zero all values
void clearNixie( uint16_t idx ) {
  tubes[idx].c0 = 0;
  tubes[idx].c1 = 0;
  tubes[idx].c2 = 0;
  tubes[idx].c3 = 0;
  tubes[idx].c4 = 0;
  tubes[idx].c5 = 0;
  tubes[idx].c6 = 0;
  tubes[idx].c7 = 0;
  tubes[idx].c8 = 0;
  tubes[idx].c9 = 0;
}

nixie.h

#ifndef Nixie_H
#define Nixie_H

#include <Arduino.h>

typedef struct {
  byte c0;
  byte c1;
  byte c2;
  byte c3;
  byte c4;
  byte c5;
  byte c6;
  byte c7;
  byte c8;
  byte c9;
} Nixie;

void clearNixie( uint16_t i );

#endif

NixieTubes.ino

// I've written this for nixie tubes since you already have them. This should be able to run this on a Arduino Uno.
// Pin assignments live in globals.h

#include <avr/io.h>
#include <avr/interrupt.h>
#include "globals.h"

volatile byte bit= 128;
volatile Nixie  tubes[MAX_TUBES];

void setup() {

  pinMode( LATCH_PIN, OUTPUT );
  pinMode( CLOCK_PIN, OUTPUT );
  pinMode( DATA_PIN,  OUTPUT );

  // init the nixie tube values to off
  for( int i= 0; i < MAX_TUBES; i++ ) {
    clearNixie( i );
  }


  cli();
  TCCR1A = 0;
  TCCR1B = 0;

  OCR1A = DELAY;
  TCCR1B |= (1 << WGM12);
  TCCR1B |= (1 << CS12);
  TIMSK1 |= (1 << OCIE1A);

  sei();
}

// BCM
ISR(TIMER1_COMPA_vect) {

  bit   <<= 1;
  OCR1A <<= 1;

  if( bit == 0 ) {
    OCR1A = DELAY;
    bit  = 1;
  }

  // Latch LOW
  PORTB &= ~B00000001;

  int i= MAX_TUBES - 1;
  while( i != -1 ) {

    // Character: 0
    if( tubes[ i ].c0 & bit )
        PORTB &= ~B00001000;
    else
        PORTB |=  B00001000;
    // toggle clock
    PORTB |=  B00010000;
    PORTB &= ~B00010000;

    // Character: 1
    if( tubes[ i ].c1 & bit )
        PORTB &= ~B00001000;
    else
        PORTB |=  B00001000;
    // toggle clock
    PORTB |=  B00010000;
    PORTB &= ~B00010000;

    // Character: 2
    if( tubes[ i ].c2 & bit )
        PORTB &= ~B00001000;
    else
        PORTB |=  B00001000;
    // toggle clock
    PORTB |=  B00010000;
    PORTB &= ~B00010000;

    // Character: 3
    if( tubes[ i ].c3 & bit )
        PORTB &= ~B00001000;
    else
        PORTB |=  B00001000;
    // toggle clock
    PORTB |=  B00010000;
    PORTB &= ~B00010000;

    // Character: 4
    if( tubes[ i ].c4 & bit )
        PORTB &= ~B00001000;
    else
        PORTB |=  B00001000;
    // toggle clock
    PORTB |=  B00010000;
    PORTB &= ~B00010000;

    // Character: 5
    if( tubes[ i ].c5 & bit )
        PORTB &= ~B00001000;
    else
        PORTB |=  B00001000;
    // toggle clock
    PORTB |=  B00010000;
    PORTB &= ~B00010000;

    // Character: 6
    if( tubes[ i ].c6 & bit )
        PORTB &= ~B00001000;
    else
        PORTB |=  B00001000;
    // toggle clock
    PORTB |=  B00010000;
    PORTB &= ~B00010000;

    // Character: 7
    if( tubes[ i ].c7 & bit )
        PORTB &= ~B00001000;
    else
        PORTB |=  B00001000;
    // toggle clock
    PORTB |=  B00010000;
    PORTB &= ~B00010000;

    // Character: 8
    if( tubes[ i ].c8 & bit )
        PORTB &= ~B00001000;
    else
        PORTB |=  B00001000;
    // toggle clock
    PORTB |=  B00010000;
    PORTB &= ~B00010000;

    // Character: 9
    if( tubes[ i ].c9 & bit )
        PORTB &= ~B00001000;
    else
        PORTB |=  B00001000;
    // toggle clock
    PORTB |=  B00010000;
    PORTB &= ~B00010000;


  }

  // Latch HIGH
  PORTB |= B00000001;
}

void loop() {
  // Iterate through each tube
  for( int i= 0; i < MAX_TUBES; i++ ) {
    // Count rapidly from 0 - 9
    tubes[i].c0 = 255;
    delay(100);
    tubes[i].c0 = 0;

    tubes[i].c1 = 255;
    delay(100);
    tubes[i].c1 = 0;

    tubes[i].c2 = 255;
    delay(100);
    tubes[i].c2 = 0;

    tubes[i].c3 = 255;
    delay(100);
    tubes[i].c3 = 0;

    tubes[i].c4 = 255;
    delay(100);
    tubes[i].c4 = 0;

    tubes[i].c5 = 255;
    delay(100);
    tubes[i].c5 = 0;

    tubes[i].c6 = 255;
    delay(100);
    tubes[i].c6 = 0;

    tubes[i].c7 = 255;
    delay(100);
    tubes[i].c7 = 0;

    tubes[i].c8 = 255;
    delay(100);
    tubes[i].c8 = 0;

    tubes[i].c9 = 255;
    delay(100);

    // Fade out 9
    for (int j = 255; j>0; j--) {
      tubes[i].c9 = j;
      delay(4);
    }
  }

}