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?
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 he tries so hard to impress Polly. Not to mention the bit where Polly has him thrown over her shoulder and carries him 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 Nightmare Fuel 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 irresistably 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.
Snuffintroduces 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.