What about those songs where the original version is far less popular/known than the cover?
Examples:
"Sister Morphine" came out on the Rolling Stone's Sticky Finger album in 1971. I like the Marianne Faithful version more, but when it was released in 1969 the lyrics were deemed too controversial and the album was actually banned in some places.
"The Rose" is listed on a number of uniformed websites as being written by Bette Midler. She performed the most popular version of the song, but it was written by Amanda McBroom; I actually prefer McBroom's version of the song.
I know Jackson Browne can't stand the fact that the Eagle's cover of "Take it Easy" was much more popular than his.
Also, what about "covers" which are only loosely based on another song, such as Patti Smitth's "Gloria" which is a take off on Van Morrison's song of the same name.