square thumbs?

No, you'll need to create the plugin for that. It's not meant to be part of the core product. There is already a task made for that and I believe it's marked "Field of Dreams" meaning the core dev team has no intention of coding it themselves or it's extremely low priority if one of them happens to have an interest in that plugin. Someone else will probably need to get to it first.
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http://sourceforge.net/apps/trac/gallery/ticket/445
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modules/gallery/helpers/gallery_installer.php defines these rules:

    graphics::add_rule(
      "gallery", "thumb", "resize",
      array("width" => 200, "height" => 200, "master" => Image::AUTO),
      100);
    graphics::add_rule(
      "gallery", "resize", "resize",
      array("width" => 640, "height" => 480, "master" => Image::AUTO),
      100);

Note that includes the default values. When you change your settings, we remove and re-add the rules. There's no separate rule for album vs. photo thumbnail. We call graphics::generate() in modules/gallery/helpers/graphics.php to run the rules for any given item.

---
Problems? Check gallery3/var/logs
bugs/feature req's | upgrade to the latest code | use git | help! vote!

I'm not seeing that. My photos are proportional as well as the album thumbs.
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No idea. I'm using a completely unmodified B2 at the moment.
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Yes, they are now all not in the way I want them to be... Story is as following:

a) I have square thumbs in my gallery 2. My guess from the looking at the code, import process imports data as is meaning if there is a thumb in G2 which is square, import would pick it as is. This does not apply to albums since thumbs are dynamic

b) Last night I did dump everything from thumbs and resizes folders which caused all the pictures goes bad/missing. Following up on the problem I have seen the suggestion to adjust thumb and resize dimensions on the theme options page (200->201->200, 640->639->640) and then rebuild the pictures.
Well... it did not go well because code in graphics.php does not recreate the folder structure...
Ok... after some research I did the following adjustments in modules/gallery/helpers/graphics.php (true would force folder structure):

(Update 6:28pm) - improved handling of the folder recreation

Added a new function

/**
 * Checks if folder for specified file exists otherwise creates necessary folder structure
 * @param string $path
 */
static function ensure_path($path) {
  try {
    $folder = dirname($path);
    if (!file_exists($folder)) {
      Kohana::log("error", "Missing folder detected {" . $folder . "}. Recreated." );
      mkdir($folder, 0777, true);
    }
  } catch (Exception $e) {
    // Something went wrong.
    Kohana::log("error", "Caught exception ensuring the path: {" . $path . " -> " . $folder . "}\n" . $e->getMessage() . "\n" . $e->getTraceAsString());
  }
}

Adjusted following parts of the code

static function generate...
...
if ($item->thumb_dirty) {
  $ops["thumb"] = $item->thumb_path();
  self::ensure_path($item->thumb_path());}
if ($item->resize_dirty && !$item->is_album() && !$item->is_movie()) {
  $ops["resize"] = $item->resize_path();
  self::ensure_path($item->resize_path());
}

static function resize...
...
} else {
  // ensure that folder exists
  self::ensure_path($output_file));
  Image::factory($input_file)

That may not be final solution, or could be overkill, but it does what it is suppose to do - allows recreate proper folder structure and refresh all resizes/thumbs.

This is today. Last night I have created a case http://sourceforge.net/apps/trac/gallery/ticket/550
and I am hopelessly (Field of Dreams) looking forward to have case http://sourceforge.net/apps/trac/gallery/ticket/445 implemented or for any information what I have to modify to force square thumbs

To say everything is here in code - classes support crop properly, but I am having difficulty as well to find where crop could be called instead of resize for thumbs...

Ok, will continue there