This Gist shows how to set the application titlebar colors. There is a helper function that accepts an HTML hexString and converts it to an RGBA color object for Windows.

changeAppTitleBarColors.js

/*
    This function expects two hexStrings and relies on hexStrToRGBA to convert
    to a JSON object that represents RGBA for the underlying Windows API to 
    understand.

    Examples of valid values: 
    setAppBarColors('#FFFFFF','#000000');
    setAppBarColors('#FFF','#000');
    setAppBarColors('FFFFFF','000000');
    setAppBarColors('FFF','000');

*/

function setAppBarColors(brandColorHex, brandColorInactiveHex) {
   // Detect if the Windows namespace exists in the global object
   if (typeof Windows !== 'undefined' &&
            typeof Windows.UI !== 'undefined' &&
            typeof Windows.UI.ViewManagement !== 'undefined') {
        var brandColor = hexStrToRGBA(brandColorHex);
        var brandColorInactive = hexStrToRGBA(brandColorInactiveHex);
        // Get a reference to the App Title Bar
        var appTitleBar = Windows.UI.ViewManagement.ApplicationView.getForCurrentView().titleBar;
        
        var black = hexStrToRGBA('#000');
        var white = hexStrToRGBA('#FFF');

        appTitleBar.foregroundColor = white;
        appTitleBar.backgroundColor = brandColor;

        appTitleBar.buttonForegroundColor = white;
        appTitleBar.buttonBackgroundColor = brandColor;

        appTitleBar.buttonHoverForegroundColor = white;
        appTitleBar.buttonHoverBackgroundColor = brandColor;

        appTitleBar.buttonPressedForegroundColor = brandColor;
        appTitleBar.buttonPressedBackgroundColor = white;

        appTitleBar.inactiveBackgroundColor = brandColorInactive;
        appTitleBar.inactiveForegroundColor = brandColor;

        appTitleBar.buttonInactiveForegroundColor = brandColor;
        appTitleBar.buttonInactiveBackgroundColor = brandColorInactive;

        appTitleBar.buttonInactiveHoverForegroundColor = brandColor;
        appTitleBar.buttonInactiveHoverBackgroundColor = brandColorInactive;

        appTitleBar.buttonPressedForegroundColor = brandColor;
        appTitleBar.buttonPressedBackgroundColor = brandColorInactive;
    }
}
// Helper function to support HTML hexColor Strings
function hexStrToRGBA(hexStr){
  // RGBA color object
  var colorObject = { r: 255, g: 255, b: 255, a: 255 };
    
  // remove hash if it exists
  hexStr = hexStr.replace('#', '');
  
  if (hexStr.length === 6) {
    // No Alpha
    colorObject.r = parseInt(hexStr.slice(0, 2),16);
    colorObject.g = parseInt(hexStr.slice(2, 4),16);
    colorObject.b = parseInt(hexStr.slice(4, 6),16);
    colorObject.a = parseInt('0xFF',16);
  } else if (hexStr.length === 8) {
    // Alpha
    colorObject.r = parseInt(hexStr.slice(0, 2),16);
    colorObject.g = parseInt(hexStr.slice(2, 4),16);
    colorObject.b = parseInt(hexStr.slice(4, 6),16);
    colorObject.a = parseInt(hexStr.slice(6, 8),16);
  } else if (hexStr.length === 3) {
    // Shorthand hex color
    var rVal = hexStr.slice(0, 1);
    var gVal = hexStr.slice(1, 2);
    var bVal = hexStr.slice(2, 3);
    colorObject.r = parseInt(rVal + rVal,16);
    colorObject.g = parseInt(gVal + gVal,16);
    colorObject.b = parseInt(bVal + bVal,16);
  } else {
    throw new Error('Invalid HexString length. Expected either 8, 6, or 3. The actual length was ' + hexStr.length);
  }
  return colorObject;
}

// Initialize when the Window loads
addEventListener('load', function(){
  var brandColor = '#16A085';
  var brandColorInactive = '#ECF0F1';
  setAppBarColors(brandColor,brandColorInactive);
});