You know, tru_faith_lost has an awesome theory - where Dean's soul was sent to Hell (uh, just cuz Kripke said. I argued.), and Lillith sent Ruby away, and then fled, thus killing the already dead host. Now, she thought of an awesome way to keep Dean's body functional while still keeping Ruby in the game (cuz Kripke said she's gonna still be around) - which is Ruby possessing Dean's body.
I think it's an awesome idea ;)
About Ruby wanting Sam to "trip the switch" - yeah, that's gonna come into play =)