Check out this article on films ghost-directed by people other than the person credited. A lot of this is rumor, although the article features links backing up its claims.
I would dispute the claims on Poltergeist, given that Steven Spielberg is known to be a hands-on producer, Tobe Hooper is a distinguished horror director (as opposed to the lesser known directors of other projects on the list) and in the eighteen years since the film’s release Hooper still maintains that he directed it.
An interesting case is made for A Prairie Home Companion, which is credited to Robert Altman (as his last film) but may have actually been directed by Paul Thomas Anderson. From the article:
The influence that director Robert Altman had over Paul Thomas Anderson can be clearly seen when you put the likes of Nashville and Magnolia side by side. Altman was 80 years old and in a frail state when he tackled what would turn out to be his final film, A Prairie Home Companion, and apparently unable to undertake much of the physical side of directing a film.
Reports around the time of the film’s production suggested that Anderson was ultimately brought on board to ghost direct the film. Thus, the suggestion was that Altman watched what was happening on monitors and gave out orders, but that Anderson was tackling the hands-on work, and dealing with the actors themselves.
Other reports argue that, as is quite common with directors of advanced age, Anderson was actually on stand-by to take over the film if Altman couldn’t. As it stood, Altman got sole directing credit for the film, in line with DGA rules.