One of the main reason why WordPress is so popular is the amount of available Plugins. Most users using Plugins via the most popular way - in the folder
wp-content, and activate them in the backend of WordPress. For other possibilities of plugin integration WordPress 3.0 try to provide a more user friendly way.
WordPress offers many possibilities to hook into the system, sometime they are better and faster.
For this reason the admin can find a new tab on the Plugin page "Drop-ins", see screenshot below of the current beta 1.