I've answered a [similar Question][1]. Basically:

 - create a [Dropin][2] plugin at the root of `wp-content` named `install.php`

 - inside `install.php`, create a new version of the pluggable function [`wp_install_defaults()`][3]

 - remove all unwanted defaults and customize at will, like:
 
 > - `update_option('template', 'your-theme');`

 > - `update_option('stylesheet', 'your-theme');`

 > - `update_option('current_theme', 'Your Theme');`

 > - `update_option('my_theme_options', $theme_options_array );`

 > - [auto-activate][4] some bundled plugins

 - bundle everything into one package (WordPress files and content files: Theme, Plugins, `install.php`)

 - now, whenever you run a install, the Dropin will be processed and the new site starts up with your pre-configurations

----
I did some more tests in my development environment and updated the [**Gist**][5] from the other answer with a working `install.php`.  
Now it contains the function *`wpse_4041_run_activate_plugin($plugin)`* (to activate bundled plugins) and an empty *`wp_new_blog_notification()`* (which is another pluggable and prevents WP from sending a notification email about the site installation).

I used the theme [F8 Lite][6] for testing. Most of the code is an adaptation of the original script (default Page, Post, Comment, Category, Blogroll). And at the end, my custom commands (change theme, set theme options, activate plugins, set plugin options). 

Check the comments on the file.

----
Not sure if it's the best method, but inside the theme `functions.php` file I put this script that will **delete** the file `wp-content/install.php`. It will run only once (based on [this Answer][7] by @bainternet) and after WP has been installed.

    // If the option doesn't exist and the install script is there, delete it
    if ( wpse_25643_run_once( 'my_custom_install_2013' ) )
    {
        if( file_exists( WP_CONTENT_DIR.'/install.php' ) ) 
    	{
            unlink( WP_CONTENT_DIR.'/install.php' );
        }
    }
       
    /**
     * Check if option exist
     *
     * @param string $key
     * @return boolean
     **/
    function wpse_25643_run_once( $key )
    {
        $test_case = get_option( 'run_once' );
    
        if ( isset( $test_case[$key] ) && $test_case[$key] )
    	{
            return false;
        }
    	else
    	{
            $test_case[$key] = true;
            update_option( 'run_once', $test_case );
            return true;
        }
    }

----
Related Q&A with another method that doesn't use `install.php`:  
http://wordpress.stackexchange.com/q/1714/12615 

  [1]: http://wordpress.stackexchange.com/a/75436/12615
  [2]: http://hakre.wordpress.com/2010/05/01/must-use-and-drop-ins-plugins/
  [3]: http://core.trac.wordpress.org/browser/tags/3.5/wp-admin/includes/upgrade.php#L93
  [4]: http://wordpress.stackexchange.com/q/4041/12615
  [5]: https://gist.github.com/4242948
  [6]: http://wordpress.org/extend/themes/f8-lite
  [7]: http://wordpress.stackexchange.com/a/25667/12615