After reading a bunch of tips for running a `WP_Query` filtering by serialized arrays, here's how I finally did it: by creating an array of comma separated values using implode in conjunction with a `$wpdb` custom SQL query utilizing `FIND_IN_SET` to search the comma separated list for the requested value.

**1. In functions.php:**

In your functions.php file (or wherever you're setting up the meta box) in the `yourname_save_post()` function use

    update_post_meta($post->ID, 'checkboxArray', implode(",", $checkboxArray)); //adding the implode

to create the array containing comma separated values.

You'll also want to change your output variable in the `yourname_post_meta()` admin meta box construction function to

    $checkboxArray = explode(",", get_post_custom($post->ID)["checkboxArray"][0]); //adding the explode

**2. In the template PHP file:**

Test: if you run a `get_post_meta( $id );` you should see `checkboxArray` as an array containing your comma separated values instead of a serialized array.

_Now, we build our custom SQL query using `$wpdb`._

    global $wpdb;

    $search = $post->ID;

    $query = "SELECT * FROM wp_posts
              WHERE FIND_IN_SET( $search, (
                  SELECT wp_postmeta.meta_value FROM wp_postmeta
                  WHERE wp_postmeta.meta_key = 'blogLocations'
                  AND wp_postmeta.post_id = wp_posts.ID )
              )
              AND ( wp_posts.post_type = 'post' )
              AND ( wp_posts.post_status = 'publish' );";

    $posts = $wpdb->get_results($query);

    foreach ($posts as $post) {
        //your post content here
    }

Notice the `FIND_IN_SET`, that's where the magic happens.

Now... since I'm using `SELECT *` this returns _all the post data_ and within the `foreach` you can echo out what you want from that (do a `print_r($posts);` if you don't know what's included. It doesn't set up "the loop" for you (I prefer it this way), but it can easily be modified to set up the loop if you prefer (take a look at `setup_postdata($post);` in the codex, you'll probably need to change `SELECT *` to select only post ID's and `$wpdb->get_results` to the correct `$wpdb` type -- see the codex for `$wpdb` also for information on _that_ subject).

Whelp, it took a bit of effort, but since `wp_query` doesn't support doing `'compare' => 'IN'` serialized or comma separated values this shim is your best option!

Hope this helps someone.