RML (Real Media Library) is one of the most wanted media wordpress plugins. It is easy to use and it allows you to organize your thousands of images in folders. It is similar to wordpress categories like in the posts.
Use your mouse (or touch) to drag and drop your files. Create, rename, delete or reorder your folders If you want to select a image from the “Select a image”-dialog (e. g. featured image) you can filter when inserting media. Just install this plugin and it works fine with all your image and media files. It also supports multisite.
The Real Media Library offers a very nice extensibility for other developers. For example you can also install a third-party plugin to create the folders physically on your FTP server (wp-content/uploads) or to synchronize folders with Lightroom. For more have a look at the Known extensions for RML.