Numbering Image List in Gallery

Set a custom function between the gallery shortcode handler and the output. Catch the img elements and add a static counter. Then return the gallery output to WordPress.

Sample code:

add_action( 'after_setup_theme', 'wpse_74492_replace_gallery_shortcode' );

/**
 * Replace the default shortcode handlers.
 *
 * @return void
 */
function wpse_74492_replace_gallery_shortcode()
{
    remove_shortcode( 'gallery' );
    add_shortcode( 'gallery', 'wpse_74492_gallery_shortcode' );
}

function wpse_74492_gallery_shortcode( $attr )
{
    // Let WordPress create the regular gallery …
    $gallery = gallery_shortcode( $attr );

    $gallery = preg_replace_callback( '~<img~', 'wpse_74492_gallery_callback', $gallery );

    return $gallery;
}

function wpse_74492_gallery_callback( $matches )
{
    static $count = 0;
    $count += 1;

    return "<span class="gallery-number">$count</span>" . $matches[0];
}

This will insert a <span class="gallery-number">1</span> into the link. You can position it in CSS with:

.gallery-number 
{
    position: absolute;
    left:0;
    top: 1em;
}