I highly recommend using Admin Menu UI (as others have mentioned) to sort plugins into top-level menu items for categories like Security, Performance, SEO/Analytics, and anything else where you have a lot of extra functionality. For plugins that have a main control screen in the backend and a separate settings screen, I try to keep them together in sequence as submenu items. Everything on the top-level gets an appropriate, standard WP icon if the plugin author added something else. Plugins that add content types and sometimes key taxonomies will go in the posts/pages area ranked in the order of their importance/frequency of use. User guide/docs go up top below Dashboard. Simple!