David Tennant did a series of adverts for Virgin satellite TV with heavy Doctor Who references, until the BBC threatened a lawsuit.
And then there were the Prime Computer adverts in Australia which explicitly featured Tom Baker and Lalla Ward as the Doctor and Romana, and became notorious among Doctor Who fans for the open Four/Romana shipping in one of them.
The Reference Overdosed series Top 10 has a Dalek among a group of wheelchair-using characters in an accessibility protest, and the Fourth Doctor among a group of "Doctor" characters in a hospital scene.
League of Extraordinary Gentlemen: The Black Dossier has the Doctor's TARDIS visible as a detail in a map. Century: 2009 had a two panel cameo appearance by both the First and Eleventh Doctors. Century: 1969 had a similar cameo by the Second.
One panel of the bizarre Peter Milligan/ Brendan McCarthy Ocean Punk comic Freakwave included a human character in what appeared to be an empty Dalek casing.
X-Men #218 had a cameo by the Brigadier and Benton, taking the Juggernaut into custody after he caused some trouble in Edinburgh.
Hobbes: Whoa. I haven't seen such fashion disasters since John Nathan-Turnernote the producer of the series from 1980 to 1989 thought question marks were fashionable. Calvin: Well, fair play to the actors. Not a lot of men can make punctuation look decorative.
"Doctor Who" (sic) is one of a lengthy list of party guests in one of The Cornelius Chronicles, which incorporates people from many Michael Moorcock works, other literary characters, and historical figures. (Moorcock's official Doctor Who novel The Coming of the Terraphiles would later explicitly incorporate the Doctor Who universe into his Multiverse.)
Live Action TV
One morning on The Big Bang Theory, Sheldon Cooper wanted to watch Doctor Who re-runs, but other people kept distracting him. He says that now it's more like Doctor Why Bother.
In Buffy the Vampire Slayer, the Nerds Of Doom claimed at one point to own all of Doctor Who on DVD. This caused some amusement among Doctor Who fans given the number of Missing Episodes, and that many surviving stories had yet to be released on DVD at the time the Buffy episode was broadcast. Additionally, the Buffy episodes "The Wish" and "Listening to Fear" featured significant plot and conceptual similarities to, respectively, the Doctor Who stories "Inferno" and "Terror of the Autons".
In G.B.H., a major scene is set at a hotel where a (surprisingly realistic, and hilarious) Doctor Who fan convention is taking place.
Referenced in, of all things, Liv and Maddie, a Disney Channel sitcom; Liv, in order to make sure her brother Joey signs her up for the Brain Olympics (him fearing she may not be smart enough), destroys his "nerd cred":
Liv: I heard he doesn't think time travel is real. He was like, "Doctor who??"
The Macintosh game Gamma Zee uses "TARDISes" as teleporter spaces.
The teleporter pod in the ZX Spectrum game The Dark Side is Bigger on the Inside with a very TARDIS-like console (though it's square rather than hexagonal because of game engine limitations).
The JauntTrooper series has sonic screwdrivers, chameleon circuits, and transmat booths as usable objects. Whovians had an advantage in knowing that a sonic could pick locks, disable traps, and repair items; others tended to discover one of these uses and assume that was it.
The description of the Simple Red Fez in Flight Rising is simply "Fezzes are cool."
Jon is shown wearing the sixth doctor's outfit here
This strip edits an earlier SRoMG to give Jon a gas mask and replace his original Madness Mantra of "Talk?" with "Are you my mummy?" in reference to "The Empty Child".
This one edits a strip where Jon panics over not getting any e-mails or texts because he thinks there's been alien abductions. This version changes it to "Eknodine", the townspeople-wiping aliens from "Amy's Choice", and shows Garfield subsequently turning into one.
The next day, we got an edit of a strip where Garfield retorts to Jon calling him a worthless lump of blubber. His real response was "Lumps of blubber have feelings too", here it's "The Adipose are lumps of blubber, and they're Doctor Who's most popular aliens!"