How to enque js script in footer that are not in .js file?

You can just hook into wp_footer and print out your script.

<?php
add_action('wp_footer', 'wpse64534_script');
function wpse64534_script()
{
    ?>
    <script>
        $(function(){
            $('#slides').slides({
                preload: <?php echo $option1 ?>,
                generateNextPrev: <?php echo $option2 ?>
            });
                        //some other script 

        });
    </script>
    <?php
}