/ Update 04/13/2014
I now have an updated and better method to do this. Follow details in my post.
/

I currently have hosting through bluehost.com. I was surprised to see all blog notification emails were coming from username@boxXXX.bluehost.com instead of the email address defined during setup. After a lot of searching online and trying out different things, I think this bug is due to a combination of my hosting company bluehost and wordpress. I found a couple of ways to fix this -

1. Use an smtp plugin to define the Sender email. You can search for them on wordpress.
2. Create a wordpress@mydomain.com email address where mydomain.com is the domain where you are hosting wordpress. This is the default email address used by wordpress which is hard coded in the wordpress code. This is used when wordpress can’t figure out the admin email address.
3. Modify the php.ini from your bluehost cpanel to have a default email address. The reasoning behind this is that wordpress uses the php mail() function and you are defining the sender in the php settings file. By modifying this, you are defining the default email for all youu php based sites. Modify the variable to appear like the following:
   sendmail_path = “/usr/sbin/sendmail -t -i -f’myemail@mydomain.com’ “
4. Dig into the wordpress code and set the email address to your desire.

There are pros and cons on each method. Going the plugin route is the easiest way, but the con on that method is that if one looked at the header of the email, they would see the ugly bluehost email addres.

Creating the wordpress@mydomain.com address is also another easy way to fix this. The con on this method is - If you have multiple wordpress installations you only get one default admin address to share between the two install. I didn’t want that. That’s also why the third option wouldn’t work for me.

You know me, I went with the 4th option :)

You need to edit the file /wp-includes/pluggable.php located in your wordpress installation.

Search for this code snippet

if ( !isset( $from_email ) ) {  
    // Get the site domain and get rid of www.  
    $sitename = strtolower( $_SERVER['SERVER_NAME'] );  
    if ( substr( $sitename, 0, 4 ) == 'www.' ) {  
        $sitename = substr( $sitename, 4 );  
    }

    $from_email = 'wordpress@' . $sitename;  
}

and replace with the email address of your choice. e.g. myemail@mydomain.com

/*if ( !isset( $from_email ) ) {  
    // Get the site domain and get rid of www.  
    $sitename = strtolower( $_SERVER['SERVER_NAME'] );  
    if ( substr( $sitename, 0, 4 ) == 'www.' ) {  
        $sitename = substr( $sitename, 4 );  
    }

    $from_email = 'wordpress@' . $sitename;  
}*/  
$from_email = 'myemail@mydomain.com';

in the same file, look for

$wp_email = 'wordpress@' .  preg_replace('#^www.#', '', strtolower($_SERVER['SERVER_NAME']));

and replace with

//$wp_email = 'wordpress@' .  preg_replace('#^www.#', '', strtolower($_SERVER['SERVER_NAME']));  
$wp_email = 'myemail@mydomain.com';

That’s it!! Now all your notifications will go from myemail@mydomain.com instead of the ugly username@boxXXX.bluehost.com. If anybody knows of a better way to do this, do let me know.