How to structure a plugin

Note that plugins are all “controllers” by WP standards.

It depends on what the plugin is supposed to do, but in all cases I would try to separate the screen output from the PHP code as much as possible.

Here’s one way to do that easily – first, define a function that loads the template:

function my_plugin_load_template(array $_vars){

  // you cannot let locate_template to load your template
  // because WP devs made sure you can't pass
  // variables to your template :(
  $_template = locate_template('my_plugin', false, false);

  // use the default one if the theme doesn't have it
  if(!_$template)
    $_template="views/template.php";

  // load it
  extract($_vars);        
  require $template;
}

Now, if the plugin uses a widget to display data:

class Your_Widget extends WP_Widget{

  ...      
  public function widget($args, $instance){

    $title = apply_filters('widget_title', $instance['title'], $instance, $this->id_base);

    // this widget shows the last 5 "movies"
    $posts = new WP_Query(array('posts_per_page' => 5, 'post_type' => 'movie')); 

    if($title)
      print $before_title . $title . $after_title;

    // here we rely on the template to display the data on the screen
    my_plugin_load_template(array(

      // variables you wish to expose in the template
     'posts'    => $posts,          
    ));

    print $before_widget;
  }
  ...

}

The template:

<?php while($posts->have_posts()): $posts->the_post(); ?>

<p><?php the_title(); ?></p> 

<?php endwhile; ?>

Files:

/plugins/my_plugin/plugin.php           <-- just hooks 
/plugins/my_plugin/widget.php           <-- widget class, if you have a widget
/themes/twentyten/my_plugin.php         <-- template
/plugins/my_plugin/views/template.php   <-- fallback template

Where do you put your CSS, JS, images, or how do you design the container for the hooks is less important. It’s a matter of personal preference I guess.