Using Capacitive Sensing Library with a 74HC4067 multiplexer
This is way late, but for anyone who runs across this, here was my solution. The two main thing is explicitly using analog input pins (which could be quantized to digital values in the software, and making sure you have resitors on each channel being sensed. Also, ground the EN pin on the multiplexer

#include &lt;CapacitiveSensor.h&gt;

#define muxS0Pin 9  // I used these rather than 4-7
#define muxS1Pin 10
#define muxS2Pin 11
#define muxS3Pin 12

#define muxSignalPin A0      // explicitly set ro analog
#define capSenseSendPin A2   // 


#define sampleRate 10
#define n_inputs 16

int touch[n_inputs] = {};

CapacitiveSensor capSense = CapacitiveSensor( capSenseSendPin, muxSignalPin );


int readMux(int channel) {
  int controlPin[] = {muxS0Pin, muxS1Pin, muxS2Pin, muxS3Pin};

  int muxChannel[16][4] = {
    {0, 0, 0, 0}, //channel 0
    {1, 0, 0, 0}, //channel 1
    {0, 1, 0, 0}, //channel 2
    {1, 1, 0, 0}, //channel 3
    {0, 0, 1, 0}, //channel 4
    {1, 0, 1, 0}, //channel 5
    {0, 1, 1, 0}, //channel 6
    {1, 1, 1, 0}, //channel 7
    {0, 0, 0, 1}, //channel 8
    {1, 0, 0, 1}, //channel 9
    {0, 1, 0, 1}, //channel 10
    {1, 1, 0, 1}, //channel 11
    {0, 0, 1, 1}, //channel 12
    {1, 0, 1, 1}, //channel 13
    {0, 1, 1, 1}, //channel 14
    {1, 1, 1, 1} //channel 15
  };

  //loop through the 4 contol pins
  for (int k = 0; k &lt; 4; k ++) {
    digitalWrite(controlPin[k], muxChannel[channel][k]);
  }
  //read the value at the SIG pin
  return capSense.capacitiveSensor( sampleRate );
}

void setup() {
  // Very important to set control pins to output mode
  pinMode(muxS0Pin, OUTPUT);
  pinMode(muxS1Pin, OUTPUT);
  pinMode(muxS2Pin, OUTPUT);
  pinMode(muxS3Pin, OUTPUT);

  digitalWrite(muxS0Pin, LOW);
  digitalWrite(muxS1Pin, LOW);
  digitalWrite(muxS2Pin, LOW);
  digitalWrite(muxS3Pin, LOW);
  Serial.begin( 9600 );  
}

void loop() {
  byte touchIndex = 0;
  for ( byte channel = 0; channel &lt; n_inputs; ++channel ) {
    Serial.print( readMux(channel));
    Serial.print("\t");
  }
  Serial.println();
}