Robin and Starfire from Teen Titans finally hooked up long after their mutual feelings were known to their teammates, their enemies, and random nerds on the Internet (in-show). This is based on a storyline in the comics.
Green Lantern and Hawkgirl. It starts off as subtext, with them alternately bickering and rushing to each other's rescue. It grows to the point that the Genre Savvy Joker, watching Hawkgirl and Green Lantern deal with one of his booby-traps, feels the need to comment on it.
Joker: Whew! Is it just me, or is there something going on between those two? "Will Green Lantern ever admit to his feelings? Will Hawkgirl ever stop sublimating her passions with that big honking mace? Will true love conquer all?"... Not on my show!**Boom!**
The episode ends this with blatant obviousness for a cartoon. After the UST is resolved, we hear an offscreen voice say "It's about time!" — and then a cut to a woman winning the jackpot at a slot machine. Hmm...
The resurgent UST between Green Lantern and Hawkgirl, and between Green Lantern and Vixennote who Lantern started seeing while Hawkgirl had secluded herself in the aftermath of her Heel–Face Turn in Starcrossed was Left Hanging at the end of the series. However, it's confirmed in a trip to the future that they eventually have a son together, Warhawk.
Batman and Wonder Woman. However, it's more or less only unresolved on Batsy's part, due to his... "issues". Wonder Woman is very open, even aggressive, about her desire to get together with him. A comic published at the same time plays with the same concept, but goes further by showing what life would be like if Batman and Wonder Woman got together. The tension is so strong that even when they were turned into children by Morgan Le Fey, their attraction was still noticeable.
Kid Green Lantern:(to an oblivious Superman) You know, for somebody with like fifty different kinds of vision, you are so blind.
Kaeloo and Mr. Cat's relationship absolutely reeks of this. Their attraction to one another is painfully obvious, even to the other characters, who also happen to have had a few moments with the she-half of the budding couple.
Kimiko and Raimundo from Xiaolin Showdown, especially in the episode where Hannibal Bean intrudes Raimundo's head. He rests his arm on her shoulder in the cinema (only to find out that she is, in fact, Hannibal). However, since they never get together in-show, fans are left to guess on their own if it was resolved post-Grand Finale.
Eduardo and Kylie from Extreme Ghostbusters. The two have a love/hate relationship going since meeting in the first episode. Many clues were given, such as when they went out of their way to save each other and most notably when Eduardo had an intimate dream about Kylie. Unfortunately, the show was canceled before there was any resolution. Darn.
In Young Justice: The Animated Series, Superboy and Miss Martian have a lot of UST... until episode 11.
More so with Wally and Artemis...until the end of season one.
Spoofed in an episode of American Dad!, where Haley says that Stan and Roger's rivalry over who's the "big dog" is due to UST and that they should just fuck already and resolve it. At the end of the episode, they end up trying to out-act each other in a play, taking a simple kiss scene and getting arrested for public indecencynote they were still just acting though. As they cheerfully compliment each other's acting skills, Haley tells her mother "I told you they just needed to fuck."
On Curious George it's pretty obvious there's something going on between The Man With The Yellow Hat and Hot Scientist Dr. Wiseman, but sadly they're in a children's educational cartoon so they can't act upon their feelings.
It should be noted that most of the tension exists between eventual Official Couple Korra and Mako, however.
However, after Korra and Mako break up for good in Book Two, the tension fades out in the background, and the two agree that they are Better as Friends. Since Book Three, the tension is now between Korra and Asami, who develop a very close friendship over the course of the next two books. The Grand Finale resolves it as much as Nickelodeon's S&P will allow, confirming that yes, Korra and Asami are the final Official Couple.
The Spectacular Spider Man: In Episode 7, Peter takes Mary Jane Watson to the dance, and the two are clearly attracted to each other. In the next episode, she tells him they're "just friends"; however, hints remain throughout the show of a lingering attraction between them, Peter calling her "gorgeous" in his head in Season 2 for example. Since the show was cancelled after its second season, this tension was never resolved. However, since Peter and MJ are the main couple in the comics, its highly likely that they would have ended up together.
In Transformers Animated, their introductory scene together and later interactions greatly imply there was some between Optimus Prime and Elita-1/Blackarachnia, in spite of the fact that she was dating Sentinel at the time. That would go a far way into explaining why Blackarachnia held Optimus more accountable for what happened, even though it was her and Sentinel's idea to go to Archa Seven in the first place. Even then, the sexual tension between them is very blatant in opposition to their conflicting alignments.