The Eleventh Doctor once included a joke and two diagrams with proof of faster-than-light travel to convince a body of geniuses they should take his advice about how to save the world from annihilation by the Atraxi. (TV: The Eleventh Hour)
Andy Hansen once told a joke to Erimem which involved R2-D2 in the punchline. (PROSE: Arrrr...)
A running joke between Lin and Mitch was that Lin kept her phone on all the time and was an instant replier. (TV: Resolution)
Bram and Gregor Van Baalen told their amnesiac brother Tricky he was an android as a joke to relieve their boredom. (TV: Journey to the Centre of the TARDIS)
The Fourth Doctor prevented an Ectoslime from killing him by telling it a joke in an alien tongue. He later tried to translate to joke to General Ironicus ("These three aliens walk into a bar, and the first alien says...") but was interrupted before he got to the punchline. (COMIC: Doctor Who and the Iron Legion)
When the First Doctor reacted with shock to the Testimony displaying his future as the Doctor of War, the Twelfth Doctor claimed "to be fair, they cut out all the jokes." (TV: Twice Upon a Time)
Prime Minister Jo Patterson believed that the Defence Drones were joking when they refused to be shut down. A Drone responded by saying "Daleks do not make jokes." (TV: Revolution of the Daleks)
In an emergency transmission sent out by the TARDIS, the Thirteenth Doctor claimed to be 'brilliant' at telling bad jokes. (WC: Message from the Doctor)
When the Sixth Doctor rose from beneath the sand in the Matrix, he told Sabalom Glitz, 'everything round here is a bad joke.' (TV: The Ultimate Foe)
Henry van Statten joked that the Ninth Doctor and Rose Tyler broke into the Vault "in-tru-da-window". (TV: Dalek [+]Robert Shearman, adapted from Jubilee (Robert Shearman), Doctor Who series 1 (BBC One, 2005).)
The Tenth Doctor joked that he got onto the Sontaran ship in-tru-da-window. (TV: The Sontaran Stratagem)
Other realities[]
A joke was among the content downloaded to a Cybus EarPod user's brain with the daily download in Pete's World. The Tenth Doctor and Rose Tyler saw that a joke had been downloaded as the Cybus Network had connected to Rose's mobile phone, and promptly witnessed a street of people erupt into laughter. (TV: Rise of the Cybermen [+]Tom MacRae, adapted from Spare Parts (Marc Platt), Doctor Who series 2 (BBC One, 2006).)