Itsuki has a habit of standing a bit too close for comfort to Kyon for Kyon's tastes when talking. He also has several lines in the novels that seem to be outright flirtatious. According to Itsuki, if he didn't do that, Haruhi would unconsciously use her Reality Warper powers to make it happen anyway, but we know how much Itsuki likes to lie, and considering he only does it when Haruhi isn't around, that doesn't help his case any. For crying out loud, he can penetrate closed space.
The official Gag-Series The Melancholy of Haruhi-chan parodied this: for a scavenger hunt, Kyon shall find a "Wall of Heart". His solution: grabbing Itsuki and telling him he loves him! Cue to a serious Art Shift for Itsuki and a COMPLETE BREAKDOWN for Haruhi! She even doesn't hear Kyon's explanation anymore, where now the "Wall of Heart" is...
As well as in Endless Eight putting his arm around his shoulder getting really close to him and telling him he should say "I love you." to Haruhi, but taken out of context it sounds more like he's saying "I love you" to Kyon.
And in "Remote Island Syndrome" there's a scene where Kyon and Itsuki are in a hotel room together discussing something and sitting on separate beds really close to each other.
In the novels especially Itsuki makes it quite clear that he trusts and likes Kyon.
Haruhi herself being all over Mikuru. At one point in the novels she actually reached up Mikuru's skirt before Kyon intervened. Not to mention saying: "Well, I'VE decided! Mikuru-chan IS my toy!"
The future version of Mikuru seems to remember these times with nostalgia and affection.
While not as extreme, Tsuruya gives off some Les Yay vibes toward Mikuru as well.
And then there's Snow Mountain Syndrome, in which it's implied that each member of the SOS Brigade is visited by the person they sexually desire the most during the night (bearing in mind that they're trapped in a house designed to fulfil their every need and desire for eternity). While Kyon fends off a phantom Mikuru, Itsuki is visited by Kyon and Mikuru is visited by Haruhi. And to top it all off, apparently Kyon did things in Itsuki's room that he would never normally do even if he went insane.
Except, as has been mentioned elsewhere, who they liked had no influence on who appeared. The person who appeared was based on a mathematical formula devised by Yuki to give the key to escape. Secondly, Koizumi was specifically disturbed by what the version of Kyon in his room did.
And then towards the end when everything is resolved, Itsuki starts making remarks about standing by Kyon's side in the SOS Brigade.
There's Les Yay between Asakura and Yuki as well, especially in the 4th novel, where Asakura is a normal human yet still ends up stabbing Kyon to protect Yuki, with considerable lesbian undertones on Asakura's side.
As well as when she goes into Yandere mode after stabbing Kyon and says she'll eliminate anything that threatens Yuki before caressing her face.
It gets worse (or better?) when Ryoko returns to life in the 10th book, explaining that she'll be around for as long as Yuki is, for they are like reflections of one another, and she proceeds to speak of Yuki in a very lustful fashion.
Also in Haruhi-chan is Yuki and "Achakura", whose scenes together are beyond adorable.
There's more of this than one would think between Yuki and Mikuru. For example:
Mikuru's hesitant to join the brigade until she sees Yuki.
In Remote Island Syndrome, when Haruhi says that Mikuru will be the murder victim, she gets scared and hugs Yuki for protection. This was censored in the anime, though. Later, Mikuru faints and Yuki is left to tend to her at her bedside.
The seventh book has a focus on the two, and as a result mostly consists of Yuki constantly staring at Mikuru, and Mikuru getting more stuttery than usual around her. At one point they even spend the night together, not to mention make chocolates together alongside Haruhi.
The infamous "Contact Lens Removal" scene in Sigh. Keep in mind that Yuki could have probably removed the lenses from a distance, and without Haruhi noticing. But instead, she took a more... direct... approach.
At the very end of the sixth book there's a picture of the two in skimpyCat Girl outfits, with Mikuru looking adoringly at Yuki. There's even a heart above her head!
One chapter of the Haruhi-chan manga is based on "Bamboo Leaf Rhapsody". When Kyon and Mikuru are forced to sleep in Yuki's house, Mikuru has to borrow Yuki's pajamas, but leaves a few buttons undone due to differences in size. The last panel shows Yuki staring at Mikuru's cleavage.
A later chapter takes this even further. It begins with Future Mikuru entering the clubroom and telling Yuki she has to leave, making her very disappointed. Upon noticing this, Mikuru insists on her staying and eventually ends up dressing in her maid outfit and offering her tea. Kyon's eventual arrival sparks an argument between the two on whether Mikuru was better when she was helpless or when she was competent. Yuki repeatedly refers to younger Mikuru's traits as "wonderful", and the argument's aftermath involves them lying next to one another and looking extremely satisfied.