Okay, please forgive me for this, but I always thought this would be an interesting theory if it was true.
In Revenge, LeChuck claims that him and Guybrush are brothers and this is supported by the fact that the head of Guybrush's father seems to work as an ingredient for the voodoo doll. Now, Ron gave an interesting comment on this whole situation once. He said "they are brothers, but they also aren't". This gave me the idea that Guybrush and LeChuck are half-brothers. I could picture LeChuck's father being a cheating alcohlic and left his wife and went with a woman and coneived Guybrush. They soon left him though and LeChuck tracked the pair down and gruesomly murdered them in revenge.
That would explain why the father's skelton worked on LeChuck and also makes Ron's answer make quite a bit of sense. I don't know, I always thought that them being brothers was a little too much, but half brothers could put a different spin on it. Since Revenge, that whole brother concept was never mentioned again and was neither confirmed nor denyed in the games.