This patch currently works, but is work in progress.

Please follow the discussion below!

Summary of Changes

Currently the color to use for non-transparent images' background fill is hardcoded to black which provides no flexibility. Allowing the users to define a desired background color fixes this.
This PR adds two new functions setFillColor and getFillColor as well as two new helper functions and changes the functions resize and rotate to use the desired fillColor, which defaults to black preserving BC.

Testing Instructions

• Create a footage array of test files for each image file type.
  I recomment downloading my test files from the links shown below into a folder named 'testfiled' in your Joomla installation's tmp directory. These are specially prepared for this test scenario.
• Copy and paste the code below to whichever file you'd like to use for running the test. I used my component's entry file.

Example:

$files  = array(
   'GIF' => array(
      'NO transparency in input file'   => JPATH_ROOT . '/tmp/testfiles/koZs44Z.gif',  // http://i.imgur.com/koZs44Z.gif
      'WITH transparency in input file' => JPATH_ROOT . '/tmp/testfiles/kyxRLmz.gif'  // http://i.imgur.com/kyxRLmz.gif
   ),
   'PNG' => array(
      'NO transparency in input file'   => JPATH_ROOT . '/tmp/testfiles/FcoS851.png',  // http://i.imgur.com/FcoS851.png
      'WITH transparency in input file' => JPATH_ROOT . '/tmp/testfiles/VL9BgDi.png'  // http://i.imgur.com/VL9BgDi.png
   ),
   'JPG' => array(
      'NO transparency in input file'   => JPATH_ROOT . '/tmp/testfiles/TFnVnnF.jpg'   // http://i.imgur.com/TFnVnnF.jpg
   )
);

// Font styles for the renderer
$ftColors = array(
   'none'        => 'rgb(0,0,0)',
   'red'         => 'rgb(255,0,0)',
   'green'       => 'rgb(0,255,0)',
   'blue'        => 'rgb(0,0,255)',
   'azure'       => 'rgb(0,255,255)',
   'pink'        => 'rgb(255,0,255)',
   'yellow'      => 'rgb(255,255,0)',
   'white'       => 'rgb(255,255,255)',
   'transparent' => 'rgb(0,0,0)',
   // 'nonsense' => 'rgb(0,0,0)'
);

// Fill colors to pass to JImage
$bgColors = array(
   'none'        => array(),
   'red'         => array('red'   =>    255,                                   'alpha' =>  33),
   'green'       => array(                   'green' => 255,                   'alpha' =>  66),
   'blue'        => array(                                    'blue' =>  255,  'alpha' =>  99),
   'azure'       => array(                   'green' => 255,  'blue' =>  255,  'alpha' =>  33),
   'pink'        => array('red'   =>    255,                  'blue' =>  255,  'alpha' =>  66),
   'yellow'      => array('red'   =>    255, 'green' => 255,                   'alpha' =>  99),
   'white'       => array('red'   =>    255, 'green' => 255,  'blue' =>  255),
   'transparent' => array(                                                     'alpha' =>  99),
   // 'nonsense' => array('red'   => 'this', 'green' => 'is', 'blue' => 'all', 'alpha' => 'nonsense, but it works')
);

// Render image
$render = function($path, $extension, $title)
{
   // Define neutral background color for every image to show the different fill colors don't apply when there's transparency
   $neutral = 'rgb(128,128,128)';

   echo '<div style="height:310px; background:' . $neutral . '; border:1px solid black; float:left;">';
   echo $title;
   echo '<img src="' . $path . '" alt="New Image" style="border-top:1px solid black;" />';
   echo '</div>';
};

array_walk($files, function(&$inFiles, $type) use(&$render, &$bgColors, &$ftColors)
{
   array_walk($inFiles, function(&$inFile, &$transparencyType) use(&$type, &$render, &$bgColors, &$ftColors)
   {
      echo '<h2 style="clear:both; padding-top:1em">Testing image type ' . $type . ' <small>(' . $transparencyType . ')</small></h2>';

      $pathinfo = pathinfo($inFile);

      $scaleFmt = JImage::SCALE_FIT;
      $outPath  = JPATH_ROOT . '/tmp/';
      $outFile  = null;
      $outExt   = $pathinfo['extension'];
      $outType  = explode('/', getimagesize($inFile)['mime']);
      $outType  = strtoupper( array_pop($outType) );
      $outType  = $outType === 'GIF' ? IMAGETYPE_GIF : ($outType === 'PNG' ? IMAGETYPE_PNG : IMAGETYPE_JPEG);
      $outFmt   = array('width' => '420', 'height' => '240');
      $outOpts  = array('quality' => 100);

      $i = 1;
      foreach ($bgColors as $color => &$rgb)
      {
         // Resize image defining no fill color (should fall back to BLACK):
         $outFile = "{$outPath}{$pathinfo['filename']}-{$outFmt['width']}x{$outFmt['height']}-{$color}.{$outExt}";
         $jimage  = new JImage($inFile);
         $jimage
         ->setFillColor($rgb)
         ->resize($outFmt['width'], $outFmt['height'], true, $scaleFmt)
         ->toFile($outFile, $outType, $outOpts);

         $render(
            str_replace(JPATH_ROOT, '', $outFile),
            $outExt,
           '<pre style="width:100%; text-align:center; color:' . $ftColors[$color] . '"><strong>' .
            print_r("TEST {$i} ==> " . strtoupper($color) . (in_array($color, array('none','nonsense')) ? ' (falls back to BLACK)' : ''), true) .
            '</strong></pre>' .
            '<pre style="width:100%; text-align:center; color:' . $ftColors[$color] . '"><strong>fillColor: ' .
            preg_replace('/(\}|\{)/', '', str_replace(',', ', ', str_replace('"', '', json_encode($jimage->getFillColor())))) .
            '<strong></pre>'
         );

         $i += 1;
      }
   });
});

echo '<pre style="clear:both; padding-top:1em">' . print_r('Imagetest done!', true) . '</pre>';
jexit();

This will render a collection of files for every image from the footage collection.

Please report issues and code improvement suggestions!