Doctor Who (television series)

Dr Who is a BBC television science fiction series, consisting of an original series and a revived series. There's also a spinoff Torchwood.
James Dignan, 15 September 2005 & 22 December 2013, Dipesh Navsaria, 19 August 2006, and André Coutanche, 22 Augustus 2006

There are but a few times that flags are used in the series. But they seem to be used more in the current series, as I can only find references to them in the transcript of The Highlanders with Doctor number 2 and in reruns of the forgettable Delta and the Bannermen with Doctor 7.
Phil Nelson, 14 September 2005

UNIT

The third Doctor, played by Jon Pertwee, had several adventures involving UNIT (the United Nations Intelligence Taskforce, recently renamed Unified Intelligence Taskforce), and I seem to recall from that period a flag displayed on the command car of Brigadier-General Lethbridge-Stewart, played by Nicholas Courtney. It was simply the UN flag defaced with the letters "UNIT" underneath the emblem in the same color (though I also recall that flag being a much deeper shade of blue than the usual sky-blue of the UN, which might have simply been a difference thrown in by the BBC's props department to make it stand out a bit).
Steve Kramer, 24 December 2013

The revived series has had a passing reference to UNIT, but no flag. A logo appeared on some glass doors, and UNIT's own website (er - right ...) shows the same logo, though there is something different (and much more '70s!) on their home page. But no flag.
André Coutanche, 22 Augustus 2006

Bannermen

In Delta and the Bannermen (McCoy era), the villains of the week (the Bannermen) wore flags from poles attached to their backs resembling the Japanese daiymo flags.
Phil Nelson, 22 August 2006

Bonnie Prince Charlie's personal standard

Episode 2 of the Highlanders (script) mentions Prince Charlie's personal standard.

Text source: Earthbound Timelords.

At one time the BBC website for the original series had a clip from The Highlanders where the flag was displayed - one of the rare clips from the missing episodes.
Phil Nelson, 15 September 2005

Van Statten flag, tentatively identified as Dutch

In the revival series 2005 episode 6, Dalek, there is a flag shown in the central office – a horizontal tricolor – red, white and blue fringed gold, but placed in a superior position to the US flag as the two are shown. If a subnational flag or a military flag, the positions of the two would be reversed. I wonder if there might be any form of defacement.
Phil Nelson, 15 September 2005

I saw this flag, and though it was never shown unambiguously, I came to the conclusion that it was exactly what it looked like – the Dutch flag. The baddie in this episode was called Van Statten, and I assumed that he had the Dutch and U.S. flags in his office to reflect his dual heritage. (I wouldn't put a lot of money on the director knowing about relative honour positions).
André Coutanche, 15 September 2005

Doctor Who and the Union Jack/Flag

The episode The Idiot's Lantern, (2007; season 2, episode 7 of the revived show, was set in London around the time of HM Queen Elizabeth II's coronation. A blustering ex-soldier who was trying to be hyper-patriotic told Rose (the Doctor's companion):

We'll have Union Jacks left, right, and centre.

She (in her guise of being some sort of govt agent) told him:

That's the Union Flag. It's the Union Jack only when it's flown at sea.

Later on, she delivered a parting shot, telling him:

And as for you Mr Connolly, only an idiot hangs the Union Flag upside down. Shame on you!

Dipesh Navsaria, 19 August 2006, and Elias Granqvist, 20 December 2013

In the 2005 episode 9/10 — The Empty Child / The Doctor Dances) — which takes place in London during the Blitz of WWII, there's the out-of-place and out-of-time incident where Rose is wearing, of all things, a tee-shirt depicting the Union Jack. A little hard to blend into the local environment of the late 1930s/early 1940s if you ask me.
Phil Nelson, 15 September 2005

It may be noted, that here she seems to have no knowledge of the difference between the Union Flag and the Union Jack when referring to the pattern on her shirt.
Elias Granqvist, 21 December 2013

Unidentified flag-like object

In the 2005 season, in episodes 4 & 5, Aliens of London and World War III, there appears to be a flag-like object (if not a flag). The color appears to be very light red (rose?) with the full achievement of a coat-of-arms. It first appears about 40 minutes into Episode 4 and early in Episode 5. But since it is rigid (in a frame), it might just be a COA.
Phil Nelson, 15 September 2005