Honourable Mention: He Will Knock Four Times (2009 Specials)
Not strictly an 'arc', as it didn't belong to a full series and only got a proper mention once thanks to a conveniently placed psychic, but 'He Will Knock Four Times' nonetheless serves as the ominous saying that haunted David Tennant's final few episodes, beginning with Planet of the Dead. His out-of-character behaviour in the following story The Waters of Mars was something of an unspoken response to this, given that he was reticent to stick around and help the doomed inhabitants of Bowie Base One, knowing that his own 'death' was around the corner. The foreshadowed knock itself was a poignant surprise; heavily, deliberately implied to be the Master responsible for the four knocks, given his disposition for trying to off the Doctor and the nagging drumbeat he constantly hears in his head, it instead turned out to be Wilfred Mott - Donna Noble's grandfather and loyal friend to the Doctor - who heralded 10's departure, politely knocking from within a radiation chamber to be set free, not initially knowing that by doing so the Doctor would have to regenerate. Beautiful.