For a 19th-century novel, Jane Eyre contains a surprising amount of fairly obvious sexual tension. The scene in which Rochester, unwilling to let Jane return to her room, ends up clinging to her hand and acting as if he is about to kiss her comes to mind. Especially since it follows a scene in which she saves him from being burned alive in his bed.
Leafpool and Crowfeather in the third Warrior Cats series after being forced to "go their separate ways" by the freakin' Warrior Code. Also a lot of tension between them in Starlight before Crowfeather confesses his feelings at the end of the book. According to the narrator, the tension literally crackles like lightning.
For the first three books of Dora Wilk Series there's a lot of UST between Dora and Miron, made complicated by the fact that Joshua, Miron's friend, has this thing for Dora as well and she quite likes him, too. Finally in Winner Takes It AllEveryone Can See It and Joshua - who can feel their emotions due to his mental link to both of them - almost pushes them at one another. They Do.
The tension between Elphaba and Glinda, from Wicked, was rather obvious, especially after Dillmond's death, to their travels to Emerald City. They also share two farewell kisses.
The musical seems to play this up, due to the fact many of the actresses who play them act rather... Gay. They exchange many long glances, and often hold hands.
The '90s Hardy Boys / Nancy Drew crossover books included a ton of UST between Nancy and Frank, including at least one illicit kiss; it could never come to anything, of course, since they both had steady love interests in their own series.
Jane Austen's Pride and Prejudice runs on subtle but pervasive UST, at least for the second half. Before that, almost the entire story is Elizabeth's POV and she insists she's very much not interested in Darcy.
Persuasion packs a pretty good punch. The first scene where Anne and Captain Wentworth are reunited after so many years, even though they do no more than exchange awkward pleasantries, is ridiculously charged.
Patrick Rothfuss's The Name of the Wind has a fairly significant amount of UST. Main character Kvothe's collection of women (and at least a few men) who want in his pants would be the envy of any harem manga, and his obliviousness to their smoldering lust nearly makes one question the direction in which his swing set be swingin' (one opens the door in the middle of the night wearing a sheet and not much else. He couldn't be bothered). Kvothe eventually falls hard for Denna, but the fact that a) he is unable to cope with the fact that she works as a kind of courtesan and b) she is extraordinarily difficult to keep track of fuels the UST for a large percentage of the book.
There's a lot of UST between Harry and Murphy in The Dresden Files. This being the series it is, it's heavily lampshaded. In Changes, it seemed like it was going to get resolved, until a bullet punched a hole through Harry and he fell into a lake to drown and (apparently) die, about fifteen minutes before they were going to meet. He did often use cold water to deal with frustration...
In Margaret Mahy's Maddigan's Fantasia, and its TV series, Maddigan's Quest, teen protagonists Garland and Timon are ridiculously shippable, despite never flirting outright. At the end of the series, as Timon, Eden and Jewel return to their own time, the pair tell each other that they'll 'always know you'.
Oddly, Harry and Hermione have tons of UST as well... in Order of the Phoenix, specifically, and built upon lesser examples earlier. They get into arguments often yet passionately care about getting the other to ultimately agree, they get into danger together and are deeply concerned for the other's physical well-being, they go into flying hugs at various points... it got to the point in Phoenix that many people assumed a Love Triangle was being set up between the trio, and saw the actual resolution as something of a swerve. The UST completely (and a few would say meta-awkwardly) evaporates come Half Blood Prince.
Azure Bonds has Alias and Akabar bel Akash. Why exactly is he willing to put his life on the line over and over again, against dragons, evil archmages, liches, and elder gods to help this complete stranger? They actually discuss, although not very seriously, the prospect of marriage, but decide against it because he is already married to two other women, and his wives have a veto over any other prospective wives, and she has no interest in joining his seraglio.
In one of the sequel novels, it turns out that Akabar did eventually marry one of Alias' clones; she was not thrilled to learn this.
In Jack Campbell's The Lost Fleet, Geary and Desjani. They know it would be inappropriate. Which makes it all the more annoying that everyone else in the fleet find it adds extra romance.
In Jack Campbell's The Lost Stars novel Tarnished Knight, toward the end of the book, it is clear that Drakon and Iceni, despite the tensions between them, are developing this.
Inheritance Cycle. Oh, dear Guntera, those books. The most fun thing is that even AFTER the last book is over, the sexual tension between Arya/Eragon and Murtagh/Nasuada is STILL unresolved and will likely remain so. Ah, well... that's what Fan Fic is for.
At least Roran is Happily Married to Katrina, and Saphira finally found a mate in Fírnen (despite the unfortunately brief nature of their relationship).
Some levels of it in Animorphs with the Rachel/Tobias and Jake/Cassie pairings.
In A Song of Ice and Fire, there's Sandor "The Hound" Clegane and Sansa. Beginning with him making sarcastic japes and mocking innocent Sansa's ideals to breaking into her room during the night, getting drunk and sleeping in her bed while waiting for her, and then putting a knife to her throat which culminates in what looks to be an almost rape scene. Sansa gets away with just singing a song for him, and he leaves behind his bloody cloak. As of currently, Sansa has been having dreams about Sandor having a wedding night with her, constantly compares every man that makes a move on her to him, and has convinced herself that Sandor kissed her that night (he didn't) and is disappointed that he only left her with his cloak.
Sarcastic, cynical Jaime Lannister and his captor, idealistic Brienne "The Beauty" bicker and squabble incessantly at first, but are shown to think about the other frequently, in an increasingly affectionate light. Both have only ever been attracted to one person (Cersei and Renly respectively), and both are weirded out by their sudden attraction to someone else, but seem to grow into it (Jaime and Cersei have a falling out and Brienne calls out for Jaime when unconscious).
In the destroyermen series by Taylor Anderson, there is a significant amount of tension between Matt and Sandra, because while they are attracted to each other, there are only four known human females alive at the most. Resultingly, out of moral responsibility, Matt and Sandra do not formally get together for three books and Matt doesn't propose marriage until book six, by which all the tension has evaporated and Everyone Can See It.
The immense tension caused by the lack of human females in comparison to human males, plus the rumours of inter-species relationships, was a major secondary conflict for a large portion of the series thus far.
Artemis Fowl and Holly Short, especially from the fifth book The Lost Colony onward. Holly actually kisses Artemis after she heals him from near death. And in the last book, Artemis returns the favour by kissing her goodbye on the forehead before performing his Heroic Sacrifice. The series ends with Holly telling an amnesic Artemis their history, in hopes to jog his memory.
The Eighth Doctor and Fitz from BBC Book's Eighth Doctor Adventures. One book, "The Blue Angel" has Fitz admit that he wants to shag the Doctor. Another, "Eater of Wasps" has the Doctor flirting with Fitz. There's also the slashy dream sequence in "Halflife" and that's just the tip of the iceberg. It's even acknowledged by some of the other characters on occasion but nothing is ever done about it. There was also UST between the Doctor and Sam in some of the earlier books but it was eventually resolved-he wasn't interested and she got over it.
Kyri Vantage and Tobimar Silverun meet near the end of book one of The Balanced Sword trilogy and are quickly attracted to each other, but each is reluctant to say anything because they're not sure the other reciprocates and they're afraid starting a relationship will complicate their quest and so on. Thankfully, it's not dragged out until the end of the trilogy, largely because halfway through book two their friend Poplock loses patience with them and bounces up and down shouting "Just kiss already!" until they admit their feelings.
The Captain and Amicia in The Traitor Son Cycle. From the moment they see each other, the tension between them is palpable to everyone, and several times, they almost make out right where they stand. However, after they spend almost a year apart, it calms down, and they both ultimately decide that they're Better as Friends.