The show has featured as a specialist subject a number of times in the past, such as in 2004, and notably when the Telegraph's resident Doctor Who reviewer Gavin Fuller became champion during Doctor Who's 30th Anniversary in 1993.
There was also a special Doctor Who-themed version of Mastermind on 19th March 2005 as part of BBC2's Doctor Who Night the weekend before Rose was to herald the triumphant return of the show on television. The questions were set by John Leeson and the winner, Karen Davies, received the trophy from the Doctor himself, Christopher Eccleston. The actor also appeared on Junior Mastermind nearly a year later, where he was interviewed by the young contestant Sam who had chosen Doctor Who's premiere year as his specialist subject on 26th February 2006.
In addition, David Tennant had Doctor Who as his specialist subject on a celebrity edition of Mastermind for Comic Relief on 13th March 2009.
Meanwhile, back in 1988 the New Zealand version of Mastermind featured Doctor Who as the specialist subject from long-term fan Jon Preddle - you can read more about his 'adventure' on the show via the New Zealand Doctor Who Fan Club.
(with thanks to Chris Moore)