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gistfile1.js

You have ...
[1,2,3,4,5,6,7,8,9]
[1,2,3,4,5,6,7]
[1,2,3]

You want in chunks of N (say 3)
[
  [1,2,3],
  [4,5,6],
  [7,8,9],
  [1,2,3],
  [4,5,6],
  [7,1,2],
  [3]
]

<?php

/**
 * Here, we just make some fake data. 1000 arrays filled with a random
 * number of URLs.
 */
$urls_to_split_up = array();
for ($i = 0; $i < 10; $i++) {
  $random_number = rand(1, 10);
  $urls = array();
  for ($n = 0; $n < $random_number; $n++) {
    array_push($urls, "http://www." . (rand(1, microtime(true))) . ".com");
  }
  array_push($urls_to_split_up, $urls);
}

/**
 * Based on http://bastian.rieck.ru/uni/bin_packing/bin_packing.pdf
 * Algorithm #10: Best-fit with lookup table
 *
 * If you sort then your runtime will be at least O(n^2). This has a better
 * runtime of O(nK) -- ie: it's a faster algorithm than using sorting.
 */
//

// Set your target size here. Anything bigger than this will not be processed.
$MINIMUM_BATCH_SIZE = 5;

// 1. Initialize a lookup table and storage
$bin_lookup = array_fill(0, count($urls_to_split_up), $MINIMUM_BATCH_SIZE);
$bin_store  = array_fill(0, count($urls_to_split_up), array());

// 2. For all object do ....
foreach ($urls_to_split_up as $urls) {

  // 3. Let W be the current object size
  $size_of_array = count($urls);

  // 4. Search suitible bin with remaining capacity
  if ($size_of_array <= $MINIMUM_BATCH_SIZE) {
    for ($i = 0; $i < count($bin_lookup); $i++) {
      if ($size_of_array <= $bin_lookup[$i]) { break; }
    }

    // Actually store the URLs and subtract remaining capacity
    $bin_lookup[$i] = $bin_lookup[$i] - $size_of_array;
    array_push($bin_store[$i], $urls);

  }

  /**
   * Uncomment these lines if you want to also process URL arrays bigger
   * than your target size
   */

  /*
  else {
    for ($i = 0; $i < count($bin_lookup); $i++) {
      if ($bin_lookup[$i] == $MINIMUM_BATCH_SIZE) { break; }
    }
    $bin_lookup[$i] = $bin_lookup[$i] - $size_of_array;
    array_push($bin_store[$i], $urls);
  }
  */
}

// Remove unused bins
$bin_store = array_values(array_filter($bin_store));

// Display results.
print_r($bin_store);

Example Results

Array
(
    [0] => Array
        (
            [0] => Array
                (
                    [0] => http://www.696358599.com
                    [1] => http://www.1101237996.com
                    [2] => http://www.39990498.com
                    [3] => http://www.808152997.com
                )

            [1] => Array
                (
                    [0] => http://www.104638105.com
                )

        )

    [1] => Array
        (
            [0] => Array
                (
                    [0] => http://www.659977343.com
                    [1] => http://www.528424096.com
                )

            [1] => Array
                (
                    [0] => http://www.1018981549.com
                    [1] => http://www.343493509.com
                    [2] => http://www.1037396543.com
                )

        )

    [2] => Array
        (
            [0] => Array
                (
                    [0] => http://www.306146048.com
                    [1] => http://www.1275939888.com
                    [2] => http://www.1141004911.com
                    [3] => http://www.1389901513.com
                    [4] => http://www.46297440.com
                )

        )

    [3] => Array
        (
            [0] => Array
                (
                    [0] => http://www.904192341.com
                    [1] => http://www.275948608.com
                    [2] => http://www.1146600584.com
                    [3] => http://www.610914222.com
                )

        )

    [4] => Array
        (
            [0] => Array
                (
                    [0] => http://www.560237467.com
                    [1] => http://www.878781689.com
                    [2] => http://www.975916448.com
                )

        )

)