Like many here already answered It really depends on what the plugin is supposed to do, but here is my base structure:

my-plugin/
    admin/
        holds all back-end administrative files
        js/
            holds all back-end JavaScript files
        css/                    
            holds all back-end CSS files
        images/
            holds all back-end images
        admin_file_1.php        back-end functionality file
        admin_file_2.php        another back-end functionality file 
    js/
        holds all front end JavaScript files
    css/
        holds all fronted CSS files
    inc/
        holds all helper classes
    lang/                   
        holds all translation files
    images/
        holds all fronted images
    my-plugin.php               main plugin file with plugin meta, mostly includes,action and filter hooks
    readme.txt                  
    changelog.txt
    license.txt