[Galadriel: Wasn't doctor who in the Simpsons once?]
Yes, several times in fact.
---------
Honorable Mention:
In episode #3F12, 11-Feb-96, the comic book guy comes out of a "Tacomat" fast food shack with a wheelbarrow full of tacos for the "Dr. Who" marathon
------------
In episode #3F08, 26-Nov-95, when Sideshow Bob gains control over a nuclear weapon and tries to ban televison, there is a scene in an underground bunker where the representatives of TV have gathered and they are: Kent Brockman, Krusty, Chesperito, Tom Baker as The Doctor and an adult Steve Urkel.
-------
In episode #5F13, 22-Mar-1998:
Skinner: We have a very special visitor today, but he's no ordinary visitor. In fact, [almost chuckling] you might say--
Bart: He's a robot. We saw him on the way in.
Skinner: [loses enthusiasm] Thank you, Bart. All right, come in, they know.
(A Dr. Who-esque robot [on wheels] rolls into the classroom.)
Skinner: Kids, this is Robbie the Automaton.
Robot: [in robotic voice] Greetings, Earth children.
Lewis: Where are you from?
Robot: [pauses] ...Earth.
Bart soon spots a man using a remote-control running the robot and hits the man with his slingshot, causing the control to turn to "Crush, Kill, Destroy". The Doctor-bot attacks Principal Skinner, then the scene ends.
-------
In episode #AABF05, 20-Dec-1998, at a SciFi convention, you can see Tom Baker as The Doctor signing autographs with the TARDIS beside him.
This is the episode guest-starring Mark Hamill, where Homer becomes Mayor Quimby's bodyguard by saving him and Mark from rampaging nerds.
-------
In episode #BABF01, 31-Oct-1999, when Bart & Lisa gain super-powers, they come up against The Collector, who is actually, the comic book guy. He has collected several life-sized "action figures", in giant unbreakable poly-bags, who are the real actors. One of them is Tom Baker, whom The Collector mistaken refers to as Dr. Who, instead of The Doctor.
-------
OB-Wan, your friendly neighborhood research guy.