Alas, Poor Scrappy: Sam was widely considered irritating during her run. But since Fitz is so broken up about it when she's killed off-screen, you can't help but feel a little sad...
Big-Lipped Alligator Moment: Halfway through Vampire Science the Doctor and a vampire break into a hairdresser's so she can give him a haircut (with wash and conditioner). This is never mentioned again.
Bizarro Episode: The Blue Angel is by far the weirdest novel. You've got a Star TrekParody Episode, a hallucinating human-Doctor Alternate Universe, and... some ladies of a certain age going shopping? The plotlines are more or less independent of each othernote Well... the human Doctor segments are in first person and contain a lot of the Doctor fussing and worrying about various personal and philosophical quandaries, and then in one chapter the usual Doctor's storyline goes into first person and he starts fussing about existential angst, but still, the stories seem to be sealed away into little Alternate Universes relative to each other... but actually they're implied to be connected. It's complicated. and it all gets rather metafictional. The Adventuress of Henrietta Street is stylistically unusual, but the plot is only slightly more surreal than any other.
Foe Yay: The Doctor mostly just thinks it's hilarious that Sabbath literally "stole his heart", but there is quite a lot of legitimate sexual tension. Camera Obscura really lays it on thick between the Doctor and Sabbath (flirting, kissing, generally getting all up close and personal), and in Sometime Never, Sabbath actually admits he's "more than a little fond of" the Doctor. (Aww.) Well, with the Master gone, the Doctor clearly needs a recurring Friendly Enemy to have sexual tension with, right? More on the Doctor Who Foe Yay page. It seems like Lloyd Rose likes this trope, since in City of the Dead, one of the villains is a Mad Artist who makes a bit of a fuss over the Doctor's attractiveness, and another one who... well.
'[...]You're my key. Or my bait. Probably both. But in either case -' he traced a forefinger along the Doctor's long upper lip - 'you're all mine.'
The Doctor twisted away but Dupre tightened his grip, holding him still. 'You can't get free,' he said softly. 'I've made very sure of that.' He slid his hand down to the Doctor's chest.
Hilarious in Hindsight: In The Adventures Of Henrietta Street, Fitz' comments about the TARDIS being "something old, something new, something borrowed, something blue" are this after "The Big Bang".
By the end of the series, Gallifrey is destroyed and all the Time Lords have retreated into the matrix. In a 2013 issue of Doctor Who Magazine, it was revealed that the secret backstory to Scream of the Shalka, by coincidence, also involved those same plot points.
The Doctor was "more than friends" with Alan Turing and mentions having been in love with William Shakespeare.
The Doctor has a sometimes-tempestuous, sometimes-adorable relationship in The Year of Intelligent Tigers with composer Karl Sadeghi. Karl spends most of the book being very obliquely in love with him, waxing poetic about the Doctor constantlynote Karl watched the Doctor doze. He had flopped back on to the soft grass, his golden-brown hair spreading around his face. The bright sunshine highlighted the exotic whiteness of his skin.note The numen had left the Doctor: he was no longer a god of thunder, but only a beautiful man lying in the grass.
Fitz and the Doctor act Like an Old Married Couple, and Fitz admits to the fact he loves the Doctor and might like to have sex with him. Given the Doctor occasionally flirts with Fitznote Fitz gaped. ‘A sailor? I don’t believe it. Go on, give us a jig!’ The Doctor laughed. ‘Not likely – but I’ll show you my tattoo if you’re lucky.’, there's some interest there. He also did some very morally dubious things to get his version of Fitz back when he'd been lost. See the DW HoYay page for much more.
Jerkass Woobie: Some pretty awful things happen to Compassion. For example, she turns into a TARDIS, and just to make it worse, the Time Lords try to capture her for "breeding purposes". Whenever Fitz or the Doctor tries to show her any sympathy, she doesn't take it well.
Just Here for Godzilla: In the fandom, The Taint is almost universally panned as a sub-par book that's only saving grace is introducing the reader to Fitz Kreiner. It's often advised to new fans to just skim until you see his name, then read those bits.
Narm: Escape Velocity provides a certain sense of bathos in a character's death scene:
What a view! he thought, and then died as the ﬂames from the engines reached the bus which then exploded.
Stoic Woobie: The Doctor's life is basically terrible, in case previous entries in his trope list haven't already made this clear. He's rarely seen crying about it. Very rarely. Possibly only in Halflife, in which it was quite obviously helped along by the fact he was still somewhat under the influence of swapping minds with Fitz, who's significantly more emotive, and it was appropriately manlyTears of Remorse, at any rate.
Villain Decay: Sabbath. He's still a compelling, likable character despite all the more-powerful villains mocking him for being gullible, the Doctor just generally mocking him and trying to be friends with him, the bit where he takes his Morality Petto the zoo, the fact all his Mooks are apes who wear uniformsnote He must spend half his time stuffing them into their uniforms and trying to stop them from climbing things and crapping everywhere, his apparent inability to pick a pseudonym that doesn't have to do with holidays or days of the week, etc. It's just that he reaches a point of being no more menacing than any other character.
Fitz Kreiner. He was peer pressured into smoking to prove he's not some kind of rule-abiding Nazi (he's now addicted to nicotine), and worried about "getting his head kicked in" when he was three. There's a poem about it. It's almost like every EDA he's in is required to add another reason (or five) to why Fitz should be a horrible, cynical, broken person. The fact he's not is absolutely astonishing.