These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Malcolm being forced out of a job by someone even more villainous than himself.
Stewart Pearson gets a moment like this in the third season finale, when Cal"The Fucker"Richards tells him he's been fired as a joke. Sure, Stewart is an unlikeable, power-tripping master of meaningless PC hypocrisy, but he looks so...broken.
Dude, Not Funny!: Steve Fleming's ill-advised Josef Fritzl joke goes down like a lead balloon. When Olly is making the "eeeesh" face at you, you know you've gone too far.
Jamie. It's hard to believe he only appeared in three episodes.
The cover of the new TTOI book The Missing DoSAC Files includes the line "Attn of: Jamie MacDonald". And the fandom rejoiced. No, seriously, it's hard to quantify just how loved Jamie is.
"You know Julius, if I wasn't a heterosexual man, I would kiss you."
That onion bhaji didn't solely represent the 'problems' caused by Nicholson's upcoming report. Julius becomes positively lascivious when Malcolm is about.
...and in turn Malcolm tends to get physical with him: "Put your hand on mine! Try and open the door..."
At home Nicola Murray struggles with a failing marriage to a husband who doesn't pay her much attention and never seems proud of her. At work there's a man who takes a great interest in everything she does and gives her his undivided attention... alright, it may be Malcolm but you can't really blame her for developing a crush.
Any reference to scandal or public disgrace (and, being a political sitcom, there are plenty) is made slightly painful by what happened to Chris Langham after the series went out.
"I look like a disgraced geography teacher..."
Hugh's comment to Olly about not "clicking" with the PM's wife (his assertion that she'd say "he's a social spastic and very probably a registered nonce") combines this with a good measure of Hilarious in Hindsight for those of us with particularly dark senses of humour.