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 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 hiatus; "Time & Time Again" marked the 30th, "Happy Deathday" the 35th, "The Land of Happy Endings" the 40th, and both "Hunters of the Burning Stone" and "John Smith and the Common Men" the 50th ("Hunters" being an arc climax and "John Smith" a one-shot). They marked their 250th issue with "A Life of Matter and Death", and their 20th anniversary with "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.
What Could Have Been: 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 Ninth Doctor compilation The Cruel Sea that they would've been de-canonised by "The Night of the Doctor" and the whole War Doctor thing.
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 lack of enthusiasm for Doctor Who, which Marvel US saw as a cancelled series.
Mike Collins as artist on "Evening's Empire", which fell through because Mike got a monthly series with DC, 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.