Use Custom Content Type Manager (CCTM http://wordpress.org/extend/plugins/custom-content-type-manager/) to manage product variation custom fields in a WordPress site using WooCommerce (v 1.6.6 http://downloads.wordpress.org/plugin/woocommerce.1.6.6.zip)

functions.php

<?php 
 
 /* ... */
 
 /* add the below to your functions.php
    the th_ prefix is just to avoid naming collisions
    
    basically copied most of this from the cctm and woocommerce code and modified as needed
 */
 
 if ( is_admin() ) {
  require_once (ABSPATH . '/wp-content/plugins/custom-content-type-manager/includes/CCTM.php');

// only do any of this if the CCTM class is loaded
	if ( class_exists('CCTM') ) {
    
    // get the field from CCTM
		function th_get_custom_fields($post_type) {
			if (isset(CCTM::$data['post_type_defs'][$post_type]['custom_fields'])) {
				return CCTM::$data['post_type_defs'][$post_type]['custom_fields'];
			}
			else {
				return array();
			}
		}
    
		// print out the fields in the variation box
		function th_print_custom_fields($loop, $post) 
		{		
			if(!$loop)
				$loop = 0;
			$post_type = 'product_variation'; // the 7th arg from add_meta_box()
			$custom_fields = th_get_custom_fields($post_type);
			$output = '';

			// If no custom content fields are defined, or if this is a built-in post type that hasn't been activated...
			if ( empty($custom_fields) ) {
				return;
			}

			foreach ( $custom_fields as $cf ) {
				if (!isset(CCTM::$data['custom_field_defs'][$cf])) {
					// throw error!!
					continue;
				}
				$def = CCTM::$data['custom_field_defs'][$cf];

				if (isset($def['required']) && $def['required'] == 1) {
					$def['label'] = $def['label'] . '*'; // Add asterisk
				}

				$output_this_field = '';
				if (!$FieldObj = CCTM::load_object($def['type'],'fields')) {
					continue;
				}
				if ( substr($_SERVER['SCRIPT_NAME'],strrpos($_SERVER['SCRIPT_NAME'],'/')+1) == 'post-new.php' || !$post )  {	
					$def['name'] = 'variable_'.$def['name']."[$loop]";
					$FieldObj->set_props($def);
					$output_this_field = $FieldObj->get_create_field_instance();
				}
				else {
					$current_value = get_post_meta( $post->ID, $def['name'], true );
					// Check for validation errors.
					if (isset(CCTM::$post_validation_errors[ $def['name'] ])) {
						$def['error_msg'] = sprintf('<span class="cctm_validation_error">%s</span>', CCTM::$post_validation_errors[ $def['name'] ]);
						if (isset($def['class'])) {
							$def['class'] .= 'cctm_validation_error';
						}
						else {
							$def['class'] = 'cctm_validation_error';
						}

					}
					$def['name'] = 'variable_'.$def['name']."[$loop]";
					$FieldObj->set_props($def);
					$output_this_field =  $FieldObj->get_edit_field_instance($current_value);
				}

				$output .= $output_this_field;
			}

			// Print the nonce: this offers security and it will help us know when we 
			// should do custom saving logic in the save_custom_fields function
			$output .= '<input type="hidden" name="_cctm_nonce" value="'.wp_create_nonce('cctm_create_update_post').'" />';

	 		// Print the form
	 		print '<div class="form-wrap">'.$output.'</div>';

		}
		
		// show custom fields for variations in admin write panel
  		function th_product_variable_custom_fields($loop, $variation_data) {
		 	th_print_custom_fields( $loop, get_post($variation_data['variation_post_id']) );
		}
		
/*
	// working on this... getting Uncaught SyntaxError: Unexpected reserved word 
	// has something to do with the way the field is being output
	// removing $FieldObj->get_create_field_instance(); gets rid of error
	// but then of course there's no field printed...
	// see note after end of function
		function th_print_custom_fields_js() 
		{	
			$post_type = 'product_variation'; // the 7th arg from add_meta_box()
			$custom_fields = th_get_custom_fields($post_type);
			$output = '';

			// If no custom content fields are defined, or if this is a built-in post type that hasn't been activated...
			if ( empty($custom_fields) ) {

				return;
			}

			foreach ( $custom_fields as $cf ) {
				if (!isset(CCTM::$data['custom_field_defs'][$cf])) {
					// throw error!!
					continue;
				}
				$def = CCTM::$data['custom_field_defs'][$cf];

				if (isset($def['required']) && $def['required'] == 1) {
					$def['label'] = $def['label'] . '*'; // Add asterisk
				}

				$output_this_field = '';
				if (!$FieldObj = CCTM::load_object($def['type'],'fields')) {
					continue;
				}
				$def['name'] = 'variable_'.$def['name']."["+loop+"]";
				$FieldObj->set_props($def);
				$output_this_field = $FieldObj->get_create_field_instance();

				$output .= $output_this_field;
			}

			// Print the nonce: this offers security and it will help us know when we 
			// should do custom saving logic in the save_custom_fields function
			$output .= '<input type="hidden" name="_cctm_nonce" value="'.wp_create_nonce('cctm_create_update_post').'" />';

	 		// Print the form
	 		print '<div class="form-wrap">'.$output.'</div>';

		}
*/	
/*
	OK. this is ruby/rails, but may be used as a guide to get where we want to be here....
	i think we need to do something similar to the rails escape_javascript function
	run that on $output
	
	      JS_ESCAPE_MAP = {
	        '\\'    => '\\\\',
	        '</'    => '<\/',
	        "\r\n"  => '\n',
	        "\n"    => '\n',
	        "\r"    => '\n',
	        '"'     => '\\"',
	        "'"     => "\\'"
	      }

	      if "ruby".encoding_aware?
	        JS_ESCAPE_MAP["\342\200\250".force_encoding('UTF-8').encode!] = '&#x2028;'
	      else
	        JS_ESCAPE_MAP["\342\200\250"] = '&#x2028;'
	      end

	      # Escapes carriage returns and single and double quotes for JavaScript segments.
	      #
	      # Also available through the alias j(). This is particularly helpful in JavaScript responses, like:
	      #
	      #   $('some_element').replaceWith('<%=j render 'some/element_template' %>');
	      def escape_javascript(javascript)
	        if javascript
	          result = javascript.gsub(/(\\|<\/|\r\n|\342\200\250|[\n\r"'])/u) {|match| JS_ESCAPE_MAP[match] }
	          javascript.html_safe? ? result.html_safe : result
	        else
	          ''
	        end
	      end
	
*/	
		// show custom fields for variations in admin write panel (via js) [not using yet, bc i can't get it to work]
		function th_product_variable_custom_fields_js() {
		 	th_print_custom_fields_js();
		}

		if( function_exists('th_print_custom_fields') ) {
			add_action('woocommerce_product_after_variable_attributes', 'th_product_variable_custom_fields',10, 2);
		} 
		if( function_exists('th_print_custom_fields_js') ) {
			add_action('woocommerce_product_after_variable_attributes_js', 'th_product_variable_custom_fields_js',10);
		} 
	} else {
		trigger_error("Unable to load class: CCTM", E_USER_WARNING);
	}
	
	
	/**
	 * Save the variable product options andcustom fields.
	 * THIS OVERRIDES THE WOO FUNCTION FOUND IN plugins/woocommerce/admin/writepanels/writepanel-product-type-variable.php
	 * The override adds the functionality for looping through and adding any CCTM custom fields for the variation
	 *
	 * @access public
	 * @param mixed $post_id
	 * @return void
	 */
	function th_process_product_meta_variable( $post_id ) {
		global $woocommerce, $wpdb;

		if (isset($_POST['variable_sku'])) {
			
			// get and set up CCTM custom fields for processing [this is part of the override]	
			$custom_field_prefix = 'cctm_variable_';
			$custom_fields = array();
			foreach($_POST as $k=>$v) {
					if(strpos($k,$custom_field_prefix) === 0) {
					$cfname = str_replace($custom_field_prefix,"", $k);
					if( !array_key_exists($k, $custom_fields) ) {
						$custom_fields[$k] = $cfname;
					}
				}
			}
			
      // these are woo's built-in fields
			$variable_post_id 			= $_POST['variable_post_id'];
			$variable_sku 				= $_POST['variable_sku'];
			$variable_weight			= $_POST['variable_weight'];
			$variable_length			= $_POST['variable_length'];
			$variable_width				= $_POST['variable_width'];
			$variable_height			= $_POST['variable_height'];
			$variable_stock 			= $_POST['variable_stock'];
			$variable_price 			= $_POST['variable_price'];
			$variable_sale_price		= $_POST['variable_sale_price'];
			$upload_image_id			= $_POST['upload_image_id'];
			$variable_file_path 		= $_POST['variable_file_path'];
			$variable_download_limit 	= $_POST['variable_download_limit'];
			$variable_shipping_class 	= $_POST['variable_shipping_class'];
			$variable_tax_class			= $_POST['variable_tax_class'];
			$variable_menu_order 		= $_POST['variation_menu_order'];

			if (isset($_POST['variable_enabled']))
				$variable_enabled 			= $_POST['variable_enabled'];

			if (isset($_POST['variable_is_virtual']))
				$variable_is_virtual		= $_POST['variable_is_virtual'];

			if (isset($_POST['variable_is_downloadable']))
				$variable_is_downloadable 	= $_POST['variable_is_downloadable'];

			$attributes = (array) maybe_unserialize( get_post_meta($post_id, '_product_attributes', true) );

			$max_loop = max( array_keys( $_POST['variable_post_id'] ) );

			for ( $i=0; $i <= $max_loop; $i++ ) {

				if ( ! isset( $variable_post_id[$i] ) ) continue;

				$variation_id = (int) $variable_post_id[$i];

				// Virtal/Downloadable
				if (isset($variable_is_virtual[$i])) $is_virtual = 'yes'; else $is_virtual = 'no';
				if (isset($variable_is_downloadable[$i])) $is_downloadable = 'yes'; else $is_downloadable = 'no';

				// Enabled or disabled
				if (isset($variable_enabled[$i])) $post_status = 'publish'; else $post_status = 'private';

				// Generate a useful post title
				$variation_post_title = sprintf(__('Variation #%s of %s', 'woocommerce'), $variation_id, get_the_title($post_id));

				// Update or Add post
				if (!$variation_id) :

					$variation = array(
						'post_title' => $variation_post_title,
						'post_content' => '',
						'post_status' => $post_status,
						'post_author' => get_current_user_id(),
						'post_parent' => $post_id,
						'post_type' => 'product_variation',
						'menu_order' => $variable_menu_order[$i]
					);
					$variation_id = wp_insert_post( $variation );

				else :

					$wpdb->update( $wpdb->posts, array( 'post_status' => $post_status, 'post_title' => $variation_post_title, 'menu_order' => $variable_menu_order[$i] ), array( 'ID' => $variation_id ) );

				endif;

				// Update post meta
				update_post_meta( $variation_id, '_sku', esc_html( $variable_sku[$i] ) );
				update_post_meta( $variation_id, '_price', $variable_price[$i] );
				update_post_meta( $variation_id, '_sale_price', $variable_sale_price[$i] );
				update_post_meta( $variation_id, '_weight', $variable_weight[$i] );

				update_post_meta( $variation_id, '_length', $variable_length[$i] );
				update_post_meta( $variation_id, '_width', $variable_width[$i] );
				update_post_meta( $variation_id, '_height', $variable_height[$i] );

				update_post_meta( $variation_id, '_stock', $variable_stock[$i] );
				update_post_meta( $variation_id, '_thumbnail_id', $upload_image_id[$i] );

				update_post_meta( $variation_id, '_virtual', $is_virtual );
				update_post_meta( $variation_id, '_downloadable', $is_downloadable );
				
				

				if ( $variable_tax_class[$i] !== 'parent' )
					update_post_meta( $variation_id, '_tax_class', $variable_tax_class[$i] );
				else
					delete_post_meta( $variation_id, '_tax_class' );

				if ($is_downloadable=='yes') :
					update_post_meta( $variation_id, '_download_limit', $variable_download_limit[$i] );
					update_post_meta( $variation_id, '_file_path', $variable_file_path[$i] );
				else :
					update_post_meta( $variation_id, '_download_limit', '' );
					update_post_meta( $variation_id, '_file_path', '' );
				endif;
				
				// Update custom fields [this is part of the override]
				foreach($custom_fields as $post_variable_name=>$cctm_name) {
					error_log("updating custom field for $variation_id: $cctm_name will be set to ".$_POST[$post_variable_name][$i]);
					update_post_meta( $variation_id, $cctm_name, $_POST[$post_variable_name][$i] );
				}

				// Save shipping class
				$variable_shipping_class[$i] = $variable_shipping_class[$i] > 0 ? (int) $variable_shipping_class[$i] : '';
				wp_set_object_terms( $variation_id, $variable_shipping_class[$i], 'product_shipping_class');

				// Remove old taxonomies attributes so data is kept up to date
				if ( $variation_id ) {
					$wpdb->query( $wpdb->prepare( "DELETE FROM {$wpdb->postmeta} WHERE meta_key LIKE 'attribute_%%' AND post_id = %d;", $variation_id ) );
					wp_cache_delete( $variation_id, 'post_meta');
				}

				// Update taxonomies
				foreach ($attributes as $attribute) :

					if ( $attribute['is_variation'] ) :

						$value = esc_attr(trim($_POST[ 'attribute_' . sanitize_title($attribute['name']) ][$i]));

						update_post_meta( $variation_id, 'attribute_' . sanitize_title($attribute['name']), $value );

					endif;

				endforeach;
				
				

			}

		}

		// Update parent if variable so price sorting works and stays in sync with the cheapest child
		$post_parent = $post_id;

		$children = get_posts( array(
			'post_parent' 	=> $post_parent,
			'posts_per_page'=> -1,
			'post_type' 	=> 'product_variation',
			'fields' 		=> 'ids',
			'post_status'	=> 'publish'
		));

		$lowest_price = $lowest_regular_price = $lowest_sale_price = $highest_price = $highest_regular_price = $highest_sale_price = '';

		if ($children) {
			foreach ($children as $child) {

				$child_price 		= get_post_meta($child, '_price', true);
				$child_sale_price 	= get_post_meta($child, '_sale_price', true);

				// Low price
				if (!is_numeric($lowest_regular_price) || $child_price < $lowest_regular_price) $lowest_regular_price = $child_price;
				if ($child_sale_price!=='' && (!is_numeric($lowest_sale_price) || $child_sale_price < $lowest_sale_price)) $lowest_sale_price = $child_sale_price;

				// High price
				if (!is_numeric($highest_regular_price) || $child_price > $highest_regular_price) $highest_regular_price = $child_price;
				if ($child_sale_price!=='' && (!is_numeric($highest_sale_price) || $child_sale_price > $highest_sale_price)) $highest_sale_price = $child_sale_price;
			}

	    	$lowest_price = ($lowest_sale_price==='' || $lowest_regular_price < $lowest_sale_price) ? $lowest_regular_price : $lowest_sale_price;
			$highest_price = ($highest_sale_price==='' || $highest_regular_price > $highest_sale_price) ? $highest_regular_price : $highest_sale_price;
		}

		update_post_meta( $post_parent, '_price', $lowest_price );
		update_post_meta( $post_parent, '_min_variation_price', $lowest_price );
		update_post_meta( $post_parent, '_max_variation_price', $highest_price );
		update_post_meta( $post_parent, '_min_variation_regular_price', $lowest_regular_price );
		update_post_meta( $post_parent, '_max_variation_regular_price', $highest_regular_price );
		update_post_meta( $post_parent, '_min_variation_sale_price', $lowest_sale_price );
		update_post_meta( $post_parent, '_max_variation_sale_price', $highest_sale_price );

		// Update default attribute options setting
		$default_attributes = array();

		foreach ($attributes as $attribute) :
			if ( $attribute['is_variation'] ) :
				$value = esc_attr(trim($_POST[ 'default_attribute_' . sanitize_title($attribute['name']) ]));
				if ($value) :
					$default_attributes[sanitize_title($attribute['name'])] = $value;
				endif;
			endif;
		endforeach;

		update_post_meta( $post_parent, '_default_attributes', $default_attributes );

	}
		
	remove_action( 'woocommerce_process_product_meta_variable', 'process_product_meta_variable');
	add_action('woocommerce_process_product_meta_variable', 'th_process_product_meta_variable');
}
?>