Add Google Webmasters Tools verification meta tag via the themes template.php file.

This guide refers to the meta tag verification method available for Google Webmaster Tools and these instructions are specific to Drupal 7.

You can also add any other meta tag you require using this guide.

edit: Since writing this guide a module has popped up that does all this for you. You can find the Site verify module here. However, if you require a more complex approach - see the first comment for an example - or just want to learn a bit more about how it works or simply prefer the DIY approach then please do read on:

What you require:

• Google Webmasters Tools Account - sign up here: https://www.google.com/webmasters/tools/
• Custom theme (or a copy of a supplied theme) in either /sites/default/themes/ or /sites/all/themes/
• Google Webmaster Tools Verification Code (meta tag)

1) Make sure you have your Google Webmaster Tools Verification Code meta tag. It looks something like this:
<meta name="google-site-verification" content="abcdefghijklmnopqrstuvwxyz0123456789" />

2) Browse to your themes directory. If you plan to modify your theme, it is best practice to either create a new custom theme or copy an existing theme (or create a sub-theme) in your sites/default/themes/ folder. If you don't know what I mean, you ought to read up on custom themes for Drupal 7 before continuing with this guide.

3) In your themes directory, open the template.php file in an editor. If you don't have such a file, create a blank page and call it template.php.

4) To add the meta tag we will need to use template_preprocess_html.

Initially, I thought it would be possible by using the hook_html_head_alter but this will only allow already defined $head_elements to be modified or unset, so we need to first create the element and then add it using drupal_add_html_head.

Check your template.php file to see if you already have a YOUR_THEME_NAME_preprocess_html function defined. If yes, you will need to paste the code inside the function into it.
Make sure your template.php file begins with a <?php tag if you have created a new blank file.

5) Paste the function into the template.php file. Copy the code below and paste it into your template.php file:

/**
* Preprocesses the wrapping HTML.
*
* @param array &$variables
*   Template variables.
*/
function YOUR_THEME_NAME_preprocess_html(&$vars) {
  
  // Setup Google Webmasters Verification Meta Tag.
  $google_webmasters_verification = array(
    '#type' => 'html_tag',
    '#tag' => 'meta',
    '#attributes' => array(
      'name' => 'google-site-verification',
      // REPLACE THIS CODE WITH THE ONE GOOGLE SUPPLIED YOU WITH
      'content' => 'abcdefghijklmnopqrstuvwxyz0123456789',
    ),
  );
  
  // Add Google Webmasters Verification Meta Tag to head.
  drupal_add_html_head($google_webmasters_verification, 'google_webmasters_verification');
}

6) CHANGE THE FUNCTION NAME 'YOUR_THEME_NAME' TO YOUR THEME NAME eg: garland_preprocess_html

7) EDIT THE CODE

Check this line of the code and replace the code with the one google supplied you with when you added your site to the Google Webmasters Tools.

      // REPLACE THIS CODE WITH THE ONE GOOGLE SUPPLIED YOU WITH
      'content' => 'abcdefghijklmnopqrstuvwxyz0123456789',

8) Save your file and clear all caches.

9) Reload your site and check your source code to check if your meta tag has been added to the header.

10) Done!

I hope this has helped someone with the same problem as me.