Saving multiple meta values for a single key with a meta box.

fruity-fruit.php

<?php
/*
Plugin Name: Fruity Fruit
Description: An example plugin to test saving multiple meta values.
*/

add_action( 'add_meta_boxes_post', 'fruity_fruit_add_meta_boxes'       );
add_action( 'save_post',           'fruity_fruit_save_meta',     10, 2 );

function fruity_fruit_add_meta_boxes() {
	add_meta_box(
		'fruity-fruit', 
		__( 'Fruity Fruit', 'fruity-fruit' ), 
		'fruity_fruit_meta_box', 
		'post', 
		'side', 
		'core' 
	);
}

function fruity_fruit_meta_box( $object, $box ) {

	$fruits = get_post_meta( $object->ID, '_fruity_fruit' );

	foreach ( $fruits as $fruit ) echo $fruit;

	wp_nonce_field( basename( __FILE__ ), 'fruity-fruit-nonce' ); ?>

	<ul>
		<li>
			<label>
				<input type="checkbox" name="fruity-fruit[]" value="apple" <?php checked( in_array( 'apple', $fruits ), true ); ?> /> 
				<?php _e( 'Apple', 'example' ); ?>
			</label>
		</li>
		<li>
			<label>
				<input type="checkbox" name="fruity-fruit[]" value="banana" <?php checked( in_array( 'banana', $fruits ), true ); ?> /> 
				<?php _e( 'Banana', 'example' ); ?>
			</label>
		</li>
		<li>
			<label>
				<input type="checkbox" name="fruity-fruit[]" value="kiwi" <?php checked( in_array( 'kiwi', $fruits ), true ); ?> /> 
				<?php _e( 'Kiwi', 'example' ); ?>
			</label>
		</li>
		<li>
			<label>
				<input type="checkbox" name="fruity-fruit[]" value="orange" <?php checked( in_array( 'orange', $fruits ), true ); ?> /> 
				<?php _e( 'Orange', 'example' ); ?>
			</label>
		</li>
		<li>
			<label>
				<input type="checkbox" name="fruity-fruit[]" value="watermelon" <?php checked( in_array( 'watermelon', $fruits ), true ); ?> /> 
				<?php _e( 'Watermelon', 'example' ); ?>
			</label>
		</li>
	</ul>
<?php }

function fruity_fruit_save_meta( $post_id, $post = '' ) {

	if ( !is_object( $post ) )
		$post = get_post();

	if ( !isset( $_POST['fruity-fruit-nonce'] ) || !wp_verify_nonce( $_POST['fruity-fruit-nonce'], basename( __FILE__ ) ) )
		return;

	if ( defined( 'DOING_AUTOSAVE' ) && DOING_AUTOSAVE )
		return;
	if ( defined( 'DOING_AJAX' ) && DOING_AJAX )
		return;
	if ( defined( 'DOING_CRON' ) && DOING_CRON )
		return;
	if ( 'revision' === $post->post_type )
		return;

	$fruit_options = array( 'apple', 'banana', 'kiwi', 'orange', 'watermelon' );

	$meta_values = get_post_meta( $post_id, '_fruity_fruit' );

	if ( isset( $_POST['fruity-fruit'] ) && is_array( $_POST['fruity-fruit'] ) ) {

		foreach ( $_POST['fruity-fruit'] as $new_fruit ) {

			 if ( !in_array( $new_fruit, $meta_values ) )
				add_post_meta( $post_id, '_fruity_fruit', $new_fruit, false );
		}

		foreach ( $fruit_options as $old_fruit ) {

			if ( !in_array( $old_fruit, $_POST['fruity-fruit'] ) && in_array( $old_fruit, $meta_values ) )
				delete_post_meta( $post_id, '_fruity_fruit', $old_fruit );
		}
	}

	elseif ( !empty( $meta_values ) ) {
		delete_post_meta( $post_id, '_fruity_fruit' );
	}
}