A Cover Version of a song is a song that is recorded by a different artist than the original.
Cover versions are mostly used in Guitar Hero because of an artist not allowing the use of the original Master Track or otherwise not having the master track available. Cover versions are shown by the song as made famous by such as Heart-Shaped Box as made famous by Nirvana.
Guitar Hero III: Legends of Rock has significantly fewer of cover versions, since Neversoft was able to get more bands to sign up, while the series is now more famous. It should be noted that every bonus song has been a master track except for "She Bangs the Drums" in Guitar Hero III.