I think Mediabrowser has support for something like this. I remember on their wiki or setup guide something about treating multiple files as a single movie. Don't know if it applies to TV shows or episodes. Might want to look it up.
Edit: found it: http://community.mediabrowser.tv/permalinks/1003/what-are-movie-playlists-why-do-they-exist
Edit: found it: http://community.mediabrowser.tv/permalinks/1003/what-are-movie-playlists-why-do-they-exist