Ascended Fanon: Paul Cornell's Seventh Doctor story "The Chameleon Factor" is chiefly devoted to ascending the fanon that the First Doctor's ring had enigmatic powers and was some kind of psychic or technological link to the TARDIS.
Development Gag: The alternate universe spider-Daleks from "Fire and Brimstone" come from unused scripts for the project that became the TV Movie.
Development Hell: Quite a few stories got stuck in it or were vetoed altogether. One story would have seen the Eighth Doctor versus sentient paintings; another featured an earlier version of Izzy's character as a pair of twins Touched by Vorlons. The authors' notes in the comic compilations really elaborate on the writing process, with plenty of first draft scans and hand-written notes. Alan Barnes ended up recycling his vetoed ideas for the Eighth Doctor in Charley Pollard's Big Finish story arc instead (notably in "Storm Warning" and "Neverland").
Milestone Celebration: The strip began marking the show's anniversaries during the long 1989-2005 hiatus; a multi-Doctor story "Time & Time Again" marked the 30th, another multi-Doctor story "Happy Deathday" the 35th, "The Land of Happy Endings" the 40th (a homage to the TV Comics strips), and both "Hunters of the Burning Stone" and "John Smith and the Common Men" the 50th ("Hunters" being an arc climax which teams the Eleventh Doctor up with Ian and Barabara, and "John Smith" a one-shot). They marked their 250th issue with "A Life of Matter and Death", and their 20th anniversary with the Real World Episode "TV Action!". The 500th issue featured "The Stockbridge Showdown", which returned to the Stockbridge setting, featured many of the comic's past regular and recurring characters, included new art by many previous artists, and wrapped up a plotline that had been abandoned in the mid-1980s due to a change of writer. That issue also contained a supplement showcasing every magazine cover, the covers for issues 1 and 500 being bookends, the latter being a homage to the former.
Official Fan-Submitted Content: The 1995 story "Land of the Blind" used the winning entry in a DWM monster-design competition for its villains, the Vortexians. The three runner-up designs all made single-panel cameos in crowd scenes.
In the creators' notes for the Evening's Empire TPB, Andrew Cartmel apologises for the stereotypical depiction of Hollywood Satanist goths in his story "Ravens".
In the creators' notes in the Land of the Blind TPB, Nicholas Briggs apologises for the misogynistic treatment of Polly in his First Doctor story "Food for Thought", which as its nadir even refers to her in the narrative caption as the Doctor's "fashion accessory".
One potential comic would have been a multi-Doctor story, with Tenth meeting Eighth and Destrii.
Russell T Davies offered the actual Eight-Nine regeneration to the strip, but a variety of restrictions on the matter (not being able to feature the Ninth Doctor with anyone bar Rose, for example, and more importantly the whole Time War thing) led to the idea being ultimately dropped by the editorial staff, who felt they wouldn't be able to do it justice. A draft script and a drawing are available in the Eighth Doctor compilation The Flood.
They note in the commentary for the Ninth Doctor compilation The Cruel Sea that had they went with it, said regeneration would've been de-canonised by the existence of the War Doctor.
The commentary for Seventh Doctor compilation The Good Soldier reveals the following might-have-beens:
A 1989 proposal for a Seventh Doctor and Ace UK newspaper strip which didn't get commissioned due to perceived declining interest in the series and uncertainty over its future.
A ten-part Abslom Daak project by Daak's creator Steve Moore, nixed by changes at Marvel US.
A miniseries teaming up the Seventh Doctor and Doctor Strange by Andrew Cartmel, not commissioned due to Marvel US Editor-in-Chief Tom DeFalco perceiving a lack of enthusiasm for Doctor Who following its cancellation in 1989.
Mike Collins as artist on "Evening's Empire", which fell through because Mike got a monthly series with DC Comics, Peter Cannon: Thunderbolt, and had to start writing immediately.
The commentary for the Twelfth Doctor compilation The Eye of Torment includes writer Jacqueline Rayner describing the twisty path "Blood and Ice" took in development. About the only major element that didn't change was the core idea of Clara encountering one of her splinters (at the time, whether Clara would leave for good in "Last Christmas" was up in the air, so this could serve as her comic sendoff if she did). Initially it was to be an Ancient Rome-set story with villains who can turn three-dimensional objects into two-dimensional ones. Both setting and villains were rejected, the latter for being too similar to the Boneless in the soon-to-air "Flatline". From there, she came up with a story set at an underwater university ("The Poseidon Project") — this was rejected because Series 9 would have an undersea-base-under-siege story with "Under the Lake"/"Before the Flood"! She moved the university to the Arctic — where "Last Christmas" was partially set! When it was moved to the Antarctic, things fell into place.
The Seventh Doctor storyline Ground Zero was initially intended to be a continuity revamp to reestablish Seven and Ace as the current TARDIS team (after a long while of the comics jumping between Doctors), returning to Doctor Who Magazine's own continuity and continuing with this team. However, after getting the script for the TV Movie, the creative team had to significantly rework the script to serve as a finale for the Seventh Doctor instead, including giving an explanation for Ace's absence. Early ideas included Ace being injured and put into a healing stasis, but was rejected on the grounds that the new Doctor would be seen as "a callous clod" if he wasn't spending time trying to help her, and that he deserved more than being "trapped in the history of the Seventh." It was soon decided that the most fitting exit for the character was a Heroic Sacrifice.
Role-Ending Misdemeanor: Subverted with the Wotcha writer, in that it was the role being ended that resulted in the misdemeanor: the Wotcha column was abruptly Cut Short due to Executive Meddling, and in response the Wotcha writer hid an obscene message in the last column. (To wit, the final column was an acrostic which spelt out "PANINI AND BBC WORLDWIDE ARE C***S", with multiple references on the same page to secret messages and things being "hidden in plain sight".)