Skull&Bones seems more like a way to help the individual memebers, not an organisation with Big Plans. Note that kerry was/is also a member, as are a lot of Washington politicians. I think they're a bit like a union for the rich and priveledged...

Freemasons: they're ancient, and from what i've heard they're mostly think tanks and discussion groups. No serious threat imo.

Illuminati: they quit after seeing how silly they looked in that Tomb Raider movie.