WooCommerce Upsells Upsells as checkbox. When product is deleted from the cart, upsells are also deleted.

content-single-product.php

<?php
/**
 * The template for displaying product content in the single-product.php template
 *
 * Override this template by copying it to yourtheme/woocommerce/content-single-product.php
 *
 * @author      WooThemes
 * @package     WooCommerce/Templates
 * @version     1.6.4
 */

if ( ! defined( 'ABSPATH' ) ) exit; // Exit if accessed directly
?>
<?php
    /**
     * woocommerce_before_single_product hook
     *
     * @hooked woocommerce_show_messages - 10
     */
     do_action( 'woocommerce_before_single_product' );
?>

<div itemscope itemtype="http://schema.org/Product" id="product-<?php the_ID(); ?>" <?php post_class(); ?>>

    <?php
        /**
         * woocommerce_show_product_images hook
         *
         * @hooked woocommerce_show_product_sale_flash - 10
         * @hooked woocommerce_show_product_images - 20
         */
        do_action( 'woocommerce_before_single_product_summary' );
    ?>

    <div class="summary entry-summary">

        <?php
            /**
             * woocommerce_single_product_summary hook
             *
             * @hooked woocommerce_template_single_title - 5
             * @hooked woocommerce_template_single_price - 10
             * @hooked woocommerce_template_single_excerpt - 20
             * @hooked woocommerce_template_single_add_to_cart - 30
             * @hooked woocommerce_template_single_meta - 40
             * @hooked woocommerce_template_single_sharing - 50
             */
            do_action( 'woocommerce_single_product_summary' );
        ?>

        <?php global $product, $woocommerce, $woocommerce_loop; ?>

        <form action="<?php echo esc_url( $product->add_to_cart_url() ); ?>" class="cart" method="post" enctype="multipart/form-data">

            <?php do_action('woocommerce_before_add_to_cart_button'); ?>

            <?php
            if ( ! $product->is_sold_individually() )
                woocommerce_quantity_input( array(
                    'min_value' => apply_filters( 'woocommerce_quantity_input_min', 1, $product ),
                    'max_value' => apply_filters( 'woocommerce_quantity_input_max', $product->backorders_allowed() ? '' : $product->get_stock_quantity(), $product )
                ) );
            ?>

            <hr class="clear" />

            <?php

            $upsells = $product->get_upsells();

            if ( sizeof( $upsells ) == 0 ) return;

            $meta_query = $woocommerce->query->get_meta_query();

            $args = array(
                'post_type'           => 'product',
                'ignore_sticky_posts' => 1,
                'no_found_rows'       => 1,
                'posts_per_page'      => $posts_per_page,
                'orderby'             => $orderby,
                'post__in'            => $upsells,
                'post__not_in'        => array( $product->id ),
                'meta_query'          => $meta_query
            );

            $query = new WP_Query( $args );

            if ( $query->have_posts() ): ?>
                <ul>
                <?php while ( $query->have_posts() ): $query->the_post(); ?>
                    <label for="upsell_<?php the_ID(); ?>"><input type="checkbox" name="upsells[]" id="upsell_<?php the_ID(); ?>" value="<?php the_ID(); ?>" /> <?php the_title(); ?></label>
                <?php endwhile; ?>
                </ul>
            <?php endif; ?>

            <?php wp_reset_postdata(); ?>

            <button type="submit" class="single_add_to_cart_button button alt"><?php echo apply_filters('single_add_to_cart_text', __( 'Add to cart', 'woocommerce' ), $product->product_type); ?></button>
        </form>

        </div><!-- .summary -->

    <?php
        /**
         * woocommerce_after_single_product_summary hook
         *
         * @hooked woocommerce_output_product_data_tabs - 10
         * @hooked woocommerce_output_related_products - 20
         */
        do_action( 'woocommerce_after_single_product_summary' );
    ?>

</div><!-- #product-<?php the_ID(); ?> -->

<?php do_action( 'woocommerce_after_single_product' ); ?>

functions.php

<?php
/**
 * Add upsells as extra data for added product
 */
function add_upsells_to_cart( $cart_item_key ) {
    global $woocommerce;

    if ( empty( $_REQUEST['upsells'] ) || ! is_array( $_REQUEST['upsells'] ) )
        return;

    // Prevent loop
    $upsells = $_REQUEST['upsells'];
    unset( $_REQUEST['upsells'] );

    // Append each upsells to product in cart
    foreach( $upsells as $upsell_id ) {
        $upsell_id = absint( $upsell_id );

        // Add upsell into cart and set upsell_of as extra key with parent product item id
        $woocommerce->cart->add_to_cart( $upsell_id, 1, '', '', array( 'upsell_of' => $cart_item_key ) );
    }
}
add_action( 'woocommerce_add_to_cart', 'add_upsells_to_cart', 1, 6 );


/**
 * Inject upsell_of extra key cart item key when cart is loaded from session
 */
function get_cart_items_from_session( $item, $values, $key ) {
    if ( array_key_exists( 'upsell_of', $values ) )
        $item[ 'upsell_of' ] = $values['upsell_of'];

    return $item;
}
add_filter( 'woocommerce_get_cart_item_from_session', 'get_cart_items_from_session', 1, 3 );


/**
 * Remove associated upsells if product removed from cart
 */
function remove_upsells_from_cart( $cart_item_key ) {
    global $woocommerce;

    // Get cart
    $cart = $woocommerce->cart->get_cart();

    // For each item in cart, if item is upsell of deleted product, delete it
    foreach( $cart as $upsell_key => $upsell )
        if ( $upsell['upsell_of'] == $cart_item_key )
            unset( $woocommerce->cart->cart_contents[ $upsell_key ] );
}
add_action( 'woocommerce_before_cart_item_quantity_zero', 'remove_upsells_from_cart' );

Thank you for this! This saved my life.

However I had problems with the last function - removing upsells from the cart. I changed the hook to woocommerce_remove_cart_item and it works now:

add_action( 'woocommerce_remove_cart_item', 'remove_upsells_from_cart' );