If your external drive is also full of TV shows and movies, you'll probably like this app that can rename all your files automatically and fetch subtitles for you.
To rename your files with FileBot, you just have to drop the files in the left pane, choose the rename pattern (or define a new one), choose where to fetch the titles (TVRage, IMDb, AniDB, ...) and let it do its thing. Your files will then be fully organised.
The app runs on Windows, Mac OS X, Linux and even in your browser. You just need to have Java installed. To download the app, go to their SourceForge page.