Lord Vetinari seems to respond to practically everything Sam Vimes says or does with a weird mix of pride and amusement. And teasing. The fact that they meet every day while Vimes has to endure Vetinari's playful manipulation either suggests Ho Yay or Foe Yay... depending on whether Vimes finally snaps and strangles him or not. It's also worthy of note that Vimes is apparently the only person that Vetinari trusts in the conventional sense, rather than the "so aware of exactly what they'll do in any situation that there's no cause for concern" sense in which he 'trusts' everyone else.
Totally out of context, but at the end of Night Watch there's an exchange. Looks like it's one-sided.
Vetinari: And if you care to come along to my office tomorrow, we can settle the-
Vimes: There's a trial tomorrow. [...] I want this bastard to hang, after all.
Vetinari: Well then, afterward we could-
Vimes: Afterward I'm going home to my family for a while.
Similarly out of context but even this troper, who is fairly critical of most Vetinari/Vimes fanworks or theories, had to raise her eyebrows at this snippet of dialogue from Jingo:
Vetinari: You're not going to handcuff me?
Vimes: Why should I do that?
Vetinari: Treason is very nearly the ultimate crime, Sir Samuel. I think I should demand handcuffs.
Vimes: All right, if you insist.
Vetinari: You haven't any shackles, by any chance?
Then there's this little conversation between Dr. Downey and Carrot in Feet Of Clay regarding Vetinari's poisoning:
Downey: I believe [Vimes] personally took over the investigation of the poisoning?
Carrot: Well, yes. But-
Downey: Didn't you think that was odd?
Carrot: No, sir. Not when I thought about it. I think he's got a sort of soft spot for the Patrician, in his way. He once said that if anyone was going to kill Vetinari he'd like it to be him.
Lord Vetinari/Drumknott is a popular ship:
Drumkott's function in the books is as a sounding-board for Vetinari to talk in a relatively open, neutral and honest way (since in his dealings with every active character, from Vimes to Ridcully, there's always an element of manipulation going on). The result on the page is that Vetinari comes across as being quite close and trusting towards his secretary. Drumknott in turn is utterly loyal and attentive to Vetinari's habits, to the point that in Snuff it's mentioned that most people would consider Drumknott's ability to interpret his master's thoughts as 'magic'.
In The Truth when it appears that Vetinari has had a breakdown and stabbed Drumknott, the latter's reaction is to be embarrassed on behalf of his employer.
Vetinari for his part is equally observant of his employee's habits - for instance, in Making Money he knows what Drumknott eats for breakfast, which raises the question of when he had the opportunity to find out.
In Unseen Academicals, Vetinari mentions that Drumkott would probably only be interested in 'a young lady prepared to dress up as a manilla envelope', which Drumknott later rather confirms by showing interest in Lady Margolotta's equally stationary-obsessed librarian. However, this has not been alluded to since, and happened in what could be interpreted as a rough patch between Vetinari and Drumknott...
The ship is sailing at full force once more after Snuff and Raising Steam. Especially after the latter, where Vetinari and Drumknott are exceptionally companionable, if not outright close.
There's also Leonard of Quirm, drawing men with careful attention to their muscles, measuring Colon's "saddlery regions". Given that he's an Affectionate Parody of Leonardo da Vinci, who himself was a bit... iffy, this isn't completely surprising.
In the subtext regions... well, Shufti and Polly do end up running an inn together, at least until Polly has to run away on another damn fool adventure with Maladict.
Shufti and Paul ended up running the inn and raising at least one kid together.
Maladicta is plainly fixated on Polly, whether or not it's in a romantic way. The way she tries so hard to impress Polly: pure Les Yay. Not to mention the bit where Polly has her thrown over her shoulder and carries her back to camp after the incident with the bag from the sky.
Tonker's reaction to seeing the newly feminine Igorina seemed a lot less like the "Okay, that's weird" reactions of the others and a lot more "Gah! She's hot!"
Sally's dialogue with Angua seems pretty flirtatious at times (suggesting that they wrestle naked in the mud, for example) and most of Angua's jealous reasons for disliking Sally strike one as the type of thing she would write in her diary about anyone else. "She's so smart, she's so pretty, she's so special."
In Hogfather: maybe just meant to be creepy rather than Ho Yay, but did anybody else notice how Teatime's attacking Medium Dave was phrased in the book? "And then Teatime was on him, pushing him irresistibly backwards until he hit the wall." Something about Teatime (possibly his Affably Evil-ness) in the tv adaptation always made me think this scene seemed a lot like a rape scene. However, Teatime acts very similarly towards Susan, so he's probably not gay. Probably.
Snuff introduces a pair of background characters who have a suspiciously Virginia Woolf and Vita Sackville-West aura about them (the book is one long string of shout-outs to English rural novelists and poets). It is perhaps legitimate in this context to return to Soul Music and re-appraise the characters of spinster schoolmistresses Miss Butts and Miss Delcross, who very carefully cultivate an aura of never having married because they are dedicated to the girls they teach at the upscale Quirm Academy for Young Ladies. Running the Disc's premier boarding school for girls, they can therefore live together and attract no suspicion.
Snuff also gives us Stratford telling Flutter to take his clothes off (ostensibly because they're covered in blood, but...) and having a conversation with him which couldn't be described because "gossip can be so cruel"...
And then, of course, Ankh-Morpork now boasts the Blue Cat Club among its places of entertainment. Its proprietor, Mr Harris, is a fully paid up Seamstress, on the grounds that un-natural acts are only natural.
The restaurant scene in the film of Going Postal shows Gilt looming over Moist in a rather creepy way. Adora looks at them in horror and sputters "You ... and him?"