TVShowTidy is a small application written in java that will help you organize your TV Show video and subtitle files.
How does it work?
Given a source folder that contains your video and subtitle files, it will match each video file with it's subtitles based on their file name. You also have the option to get each episode's name from TVDB and use it in the file name.
Once all information is gathered you choose a destination folder and whether you want to create folders for each TV show and season.
Finally you can choose to copy/move all files while renaming them according to the naming scheme of your choice.
In addition, if you have mkvmerge installed you can repack video and subtitle files in a single mkv file. Subtitle language is detected based on the file name (en.srt, es.srt etc) and then it is embeded in the mkv file under the correct language.
Enjoy