Windows/Mac/Linux: If your media library looks anything like mine, it could use a tuneup. Missing subtitles; files that XBMC or Plex won't recognise because they're not named properly; missing episode, series or movie info; the list goes on. Filebot is an open source, cross-platform batch file renaming and organisation tool that will whip your library into shape in no time.
Filebot is a breeze to use, and you can drag and drop large numbers of files onto it at once and let it do most of the work for you. It will download subtitles, automatically identify TV shows, movies and series names, and download relevant information and artwork. The app will even organise new files automatically for you so your library doesn't end up reverting to its former state. The best part is that Filebot knows the naming conventions supported by most HTPC front-end applications and media players, so it can batch rename the files for you so everything stays nicely organised.
The video tutorial above is long, but it's a great primer on how to use the app if you run into problems. Filebot can also be used as part of a fully automated media center that grabs new media as soon as it's available. It's completely free, open source, and available for Windows, Mac, and multiple flavours of Linux. Hit the link below to download, or to read more about the app's features.