Automate your WordPress installation with this WordPress "drop in" (goes in your wp-contents folder).

install.php

<?php
echo 'This has been customized!!!';

// Perform post-install customizations
if ( function_exists( 'add_action' ) ){
	add_action( 'wp_mail_content_type' , 'customize_install' );
	function customize_install(){
		
		// Switch themes
		switch_theme('twentytwelve');
		
		// Default the timezone
		update_option( 'timezone_string', 'America/Chicago' );
		
		// Increase the Size of the Post Editor
 		update_option( 'default_post_edit_rows', 40 );
 		
		// Remove Hello Dolly 
		delete_plugins( array('hello.php') );

    		// Remove default hello world post
        	wp_delete_post(1,true);

		// Remove default sample page
		wp_delete_post(2,true);

		// Remove default Mr.Wordpress comment
      		wp_delete_comment( 1, true ) ;
      	
      		// Activate Akismet
      		activate_plugin( WP_PLUGIN_DIR . '/akismet/akismet.php' );
      	
		// Update Permalinks
		update_option( 'selection','custom' );
		update_option( 'permalink_structure','/%post_id%/%postname%/' );
		global $wp_rewrite;
		$wp_rewrite->flush_rules();
		
		// Prevent new website notice
		global $phpmailer;
		$phpmailer = new PHPMailer(); // reset
	}
}

Because we've hooked wp_mail_content_type in the install.php, all of WordPress' core API is available to us to customize WordPress' installation (i.e. you have access to the global $wpdb, etc.). This is a simplified adaption of http://www.kathyisawesome.com/421/customizing-wordpress-install/.

Unlike replacing the wp_install_defaults core function (and all the subject-to-core changes overhead that comes with it), our code is just about customizations and not about replicating any existing defaults or duplicating installer prerequisites.