Please write a single answer per comment to clearly see the most popular tools. Vote on the ones you like.
There were too many options in this post and I want to see what are the really interesting ones.
To complement this post:
What file-sharing and media organizing software do you wish that existed?
It really surprised me the first time I saw the Skip intro button on a series I downloaded. It seems to work by analyzing the audio and comparing it between episodes from the same season.