Been messing with your theme? wp_head and wp_footer are required in order for all styles and scripts to be included on the page. wp_head should be the last function before </head>.
I'd look at the Twenty Twelve theme for best practices when making a theme. Also, you should look at wp_enqueue_script.
If you need more help with your theme, I suggest trying one of the other support forums as they are better suited for those types of questions.