Audience-Alienating Era: The second half of the series, when everything got so much Darker and Edgier it was difficult to recognize it as Doctor Who; Ace was converted into a '90s Anti-Hero, the Doctor was increasingly flipping between being a Demoted to ExtraPinball Protagonist or a batshit insane Machiavellian Knight Templar that was difficult to root for, and many of the best writers of the Frocks crowd, like Paul Cornell or Gareth Roberts, had stopped writing books for the line. Production problems led to So Vile a Sin, the book that killed off Roz, coming out after the books in which she was dead.
Ensemble Dark Horse: Benny. In spades. A companion for roughly two-thirds of the novels, she would later be the focus of more novels once Virgin lost the Doctor Who rights, then of a Big Finish audio-drama series. She even met the Twelfth Doctor in the 2015 novel Big Bang Generation (her inclusion was a last-minute substitute for another Adventurer Archaeologist, River Song, when Gary Russell couldn't use that character because it would have contradicted "The Husbands of River Song").
Growing the Beard: Opinions vary, naturally, but typically around the time of Benny's introduction and/or Ace's sojourn away from the TARDIS is when the quality started to level out somewhat.
In Happy Endings, written in 1996 but set in April 2010, the aging Brigadier Lethbridge-Stewart is dying of cancer and hoping to keep living for another year. Fortunately, in the course of the story, the Brig is rejuvenated and does not die. Sadly, in Real Life, the Brigadier's actor Nicholas Courtney died in February 2011 after a long battle with cancer.
The Left-Handed Hummingbird (1993) has the Doctor get put on a gurney and wheeled into a morgue with "John Doe" on his toe tag, exactly what would happen to him after his death in the 1996 movie. It also has the Arc Words, "The Healer becomes the warrior".
The same novel has one of the Aubertides tell Bernice he is the Tenth Doctor, but she realises he isn't the Doctor as he eats meat. Later the Tenth Doctor would be in the TV version of "Human Nature", by which time the Doctor was no longer a vegetarian.
The mention of "Councillor Ph'Roch" in First Frontier would just have been a throwaway pun at the time. But since the publication of Monstrous Regiment, it's got an additional aspect — Ph'Roch is yet another military officer with an item of clothing named after him.
The Dying Days establishes Queen Elizabeth II's re-coronation (she had been temporarily deposed by invading Ice Warriors) marked the start of the New New Elizabethan Age, a popular naming convention for five billion years.
Kadiatu also prefigures River Song in a lot of ways, being an occasionally recurring character who is descended from one of the Doctor's companions, was shaped into a more-than-human weapon against the Doctor but chose her own path, and has her own adventures through space and time instead of becoming a companion herself. (None of the romance stuff, though; her relationship with the Doctor is more like a cherished but Annoying Younger Sibling.)
Rescued from the Scrappy Heap: No Future, the novel that served as the series' 30th anniversary special, brought back a villain (the Meddling Monk) and an alien race (the Vardans) that were regarded by the fandom as ludicrous jokes, teamed them up, and showed how dangerous they could be in the right hands. (While simultaneously - because this is Paul Cornell, the frockiest of the frocks - being giddily affectionate about how silly they were in the first place.)
Tear Jerker: The denouement of Love and War. Watching the relationship between Ace and the Doctor disintegrate is brutal.
Too Bleak, Stopped Caring: A common critique about the books as they go on is that they become too grim. The Doctor loses his fun and playful side from the television series and becomes a callous manipulating bastard, while Ace turned into a hardened space marine who also lost all of her likeable traits and just became a hardened bitch. Throw in copious amounts of violence, sex and gore and you have one of the bleakest versions of Doctor Who ever.
What Do You Mean, It's Not for Kids?: Many bookshops shelved the first few novels with the Doctor Who Novelisations in the children's section, until Virgin pointed out that the way the novels were developing meant that it wasn't a good idea. Reported to have been consciously averted by Russell T Davies when the BBC wanted to reissue Damaged Goods to take advantage of his fame as the Show Runner of the revived series - he flatly told them that he didn't want child fans of the TV show reading it.
