This is an example of the older small-menu handling with the part of the header and .js files for the _s theme that are relevant

old-underscores-header-markup.php

<header id="masthead" class="site-header" role="banner">
	<hgroup>
		<h1 class="site-title"><a href="<?php echo home_url( '/' ); ?>" title="<?php echo esc_attr( get_bloginfo( 'name', 'display' ) ); ?>" rel="home"><?php bloginfo( 'name' ); ?></a></h1>
		<h2 class="site-description"><?php bloginfo( 'description' ); ?></h2>
	</hgroup>

	<nav role="navigation" class="site-navigation main-navigation">
		<h1 class="assistive-text"><?php _e( 'Menu', '_s' ); ?></h1>
		<div class="assistive-text skip-link"><a href="#content" title="<?php esc_attr_e( 'Skip to content', '_s' ); ?>"><?php _e( 'Skip to content', '_s' ); ?></a></div>

		<?php wp_nav_menu( array( 'theme_location' => 'primary' ) ); ?>
	</nav>
</header><!-- #masthead .site-header -->

small-menu.js

/**
 * Handles toggling the main navigation menu for small screens.
 * This is a toggle method previously used by the _s theme that utilizes jQuery and a specific browserWidth trigger.
 */
jQuery( document ).ready( function( $ ) {
	var $masthead = $( '#masthead' ),
	    timeout = false;

	$.fn.smallMenu = function() {
		$masthead.find( '.site-navigation' ).removeClass( 'main-navigation' ).addClass( 'main-small-navigation' );
		$masthead.find( '.site-navigation h1' ).removeClass( 'assistive-text' ).addClass( 'menu-toggle' );

		$( '.menu-toggle' ).click( function() {
			$masthead.find( '.menu' ).toggle();
			$( this ).toggleClass( 'toggled-on' );
		} );
	};

	// Check viewport width on first load.
	if ( $( window ).width() < 600 )
		$.fn.smallMenu();

	// Check viewport width when user resizes the browser window.
	$( window ).resize( function() {
		var browserWidth = $( window ).width();

		if ( false !== timeout )
			clearTimeout( timeout );

		timeout = setTimeout( function() {
			if ( browserWidth < 600 ) {
				$.fn.smallMenu();
			} else {
				$masthead.find( '.site-navigation' ).removeClass( 'main-small-navigation' ).addClass( 'main-navigation' );
				$masthead.find( '.site-navigation h1' ).removeClass( 'menu-toggle' ).addClass( 'assistive-text' );
				$masthead.find( '.menu' ).removeAttr( 'style' );
			}
		}, 200 );
	} );
} );