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.