This is how I ended up doing it in the end, using Requirements::javascriptTemplate():

PHP:

class Home_Controller extends Page_Controller
{
	function init()
	{
		parent::init();
		Requirements::javascript('mootools-core-1.3-full-nocompat.js');
		Requirements::javascript('slideshow.js');
		Requirements::javascriptTemplate('home.js', array(
			"slidesString" => $this->getSlidesString()
		));
	}
	
	function getSlidesString()
	{
		$slides_string = "slides = [";
		$slideshow_images = $this->SlideshowImages();
		$num_items = count($slideshow_images);
		$i = 1;
		foreach ($slideshow_images as $slideshow_image)
		{
			$imageURL = $slideshow_image->Image()->URL;
			$thumbURL = $slideshow_image->Image()->CroppedImage(50, 50)->URL;
			$slides_string .= "{imageURL:\"$imageURL\",	thumbURL:\"$thumbURL\"}";
			if ($i ++ < $num_items)
				$slides_string .= ",";
		}
		$slides_string .= "]";
		
		return $slides_string;
	}
}

This will replace the $slidesString pseudovariable in script.js with the following as a string (without the nice indentation):

slides = [
	{
		imageURL:"/site/assets/Uploads/D5120018.JPG",
		thumbURL:"/site/assets/Uploads/_resampled/croppedimage5050-D5120018.JPG"
	},
	{
		imageURL:"/site/assets/Uploads/D250007.JPG",
		thumbURL:"/site/assets/Uploads/_resampled/croppedimage5050-D250007.JPG"
	},
	{
		imageURL:"/site/assets/Uploads/DMG3025.JPG",
		thumbURL:"/site/assets/Uploads/_resampled/croppedimage5050-DMG3025.JPG"
	}
]

In script.js, I use the eval() function to execute this code, creating and populating the variable 'slides':

eval('$slidesString');

window.addEvent('domready', function()
{
	new Slideshow({slides: slides, shuffle: true});
});

I prefer this method as only the variable is generated in PHP, rather than the whole script, which is maintained in its own separate js file.