I am partial to the following plugin layout, however it usually changes depending on what the plugin requirements are.
wp-content/
plugins/
my-plugin/
inc/
Specific files for only this plugin
admin/
Files for dealing with administrative tasks
lib/
Library/helper classes go here
css/
CSS files for the plugin
js/
JS files
images/
Images for my plugin
lang/
Translation files
plugin.php
This is the main file that calls/includes other files
README
I normally put the license details in here in addition to helpful information
I have yet to create a WordPress plugin requiring a MVC style architecture but if I was to do this I would lay it out with a separate MVC directory, which itself contains views/controllers/models.