Though it sounds understated, it can mark the beginning of a change in a character or relationship.
Alice has always disliked Bob or people in general or is just very proud. But to Alice's dismay, she gets helped out by Bob in a moment when she really needs it. Glumly, Alice accepts and just when Bob is leaving Alice goes:
"Oh, and Bob..." Then a pause to indicate Alice biting the bullet. "Thank you."
This thanks, however grudging, is sincere; insincere ones fall under Embarrassing Rescue. It can often be a Crowning Moment of Heartwarming.
Compare Think Nothing of It and Does Not Know How To Say Thanks. If Bob has the same attitude as Alice, he is prone to express it, either because he dislikes the connection it formed, or because he did not act for Alice personally. Sometimes another character may apply a Prompting Nudge to get Alice to express her gratitude.
Contrast Ungrateful Bastard.
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Anime and Manga
After Zatch saves Kiyo a few times in early Zatch Bell! episodes, Kiyo tries his best to thank him but can't get the words out, settling for "I owe you". This is played more dramatically in the manga.
Seto Kaiba from Yu-Gi-Oh!, who wasn't happy about losing his World Champion's title to a virtually unknown kid, grudgingly thanks Yugi for saving his little brother Mokuba at the end of the Duelist Kingdom arc. He thanks him only for Mokuba; admitting he had to be saved himself as well would have been a too big blow to his ego.
Uryu Ishida and Ichigo Kurosaki from Bleach tend to have this kind of interaction often, though they even more frequently hang lampshades on each other's Ungrateful Bastard moments.
After taking a literal beating from their father covering for his little sister's hobby, Kousaka Kyosuke goes about his next day like any other. This trope was major character development for Kirino, including the first and so far only time she addresses him as brother and led to Kyosuke proclaimingMy Little Sister Can't be This Cute.
King Faraday delivers one (via telegram) to Batman in Batman #314 after Batman saved his life against Two-Face. Batman notes that a 'thank you' from someone like Faraday is glowing praise.
In Transmetropolitan, after Spider Jerusalem gets knocked out during a severe storm, his assistant Yelena Rossini proceeds to write a critical story in his name to make a deadline. Later, upon admitting the fact, she cringes waiting for his typical reaction (dirty words and violence), but instead he kisses her forehead and quietly replies, "Thank you."
Doctor Doom, of all people, in Doctor Strange and Doctor Doom: Triumph and Torment, thanks Strange for protecting his mother's soul from the wrath of Mephisto. It's pretty much the only hint of gratitude Strange gets during that misadventure, though.
Diego: You know, you have a way of saying "thank you" that makes it sound more like "drop dead".
Shira: It's a gift.
Films — Live-Action
In The Birds Lydia, who is always jealous of her son's love interests, thanks Melanie in this way for taking care of her after a nervous breakdown.
Corrupt Corporate Executive Zorg in The Fifth Element sort-of gives one of these to Priest Vito Cornelius after Cornelius saves him from choking on a maraschino cherry. "You saved my life. And in return I'll spare yours," and lets Cornelius leave... escorted out by his bodyguards.
Inspector Cramer does this to Nero Wolfe in The Silent Speaker. Sort of. He buys Wolfe an orchid after Wolfe saves his job.
In the first book of The Thrawn Trilogy, Mara Jade takes Luke Skywalker prisoner while walking through Myrkr and then has to protect him from the Force-hunting predators native to the planet. She hates him and is also Force-sensitive and reads as prey to the vornskrs, so she tries taking stims to go without sleep. When a vornskr does finally get past her defenses and goes for her, Luke takes back his lightsaber and saves her with considerable difficulty. She has him drop the lightsaber and back off before very grudgingly thanking him and saying that now they're even for when she did not kill him immediately after finding him. But she still hates him.
In Isaac Asimov's The Robots of Dawn, Elijah Baley receives one of these from the Chairman of Aurora, after the Chairman was prompted. The Chairman rarely thanks anyone; thanking an Earthman was... impressive.
Any time Nynaeve, Elayne, and Egwene are forced to thank Mat for anything in the Wheel of Time it comes out like this.
Turn Coat: Morgan starts to give one of these to Harry. He cuts Morgan off, stating that neither of them wants to hear him say that, for which Morgan is more than agreeable with. Earlier, Morgan also gives a grudging "You're welcome" in Dead Beat, after Harry happily thanks him for his first Warden paycheck.
In the Tom Clancy novel Patriot Games, ULA terrorist Sean Grady is temporarily transferred to a cell with ordinary criminals in it. When the cops check on him, he's been beaten and is being raped. The officer pulls the other prisoner off of Grady and gets him to the infirmary, at which point Sean says "Thanks." This is notable in that it's literally the only unnecessary word that Sean says in the presence of the police between the time he's arrested and the time he's broken out (At which point he shoots and nearly kills the officer who saved him).
One of the invading rogues on Warrior Cats gives this to the Clan cats and Tribe cats when they saved them from an eagle.
In Dorothy Gilman's The Clairvoyant Countess, Joe Painter finally manages to say "thanks" at the end of their first meeting, after Madame Karitska has stopped him from shoplifting and being caught.
McCoy: Spock, er, I know we've, er, had our disagreements. Er, maybe they're jokes, I don't know. As Jim says, we're not often sure ourselves sometimes. But, er... what I'm trying to say is... Spock: Doctor, I am seeking a means of escape. Will you please be brief? McCoy: What I'm trying to say is, you saved my life in the arena. Spock: Yes, that's quite true. McCoy: [Indignant] I'm trying to thank you, you pointed-eared hobgoblin! Spock: Oh yes, you humans have that emotional need to express gratitude. "You're welcome", I believe is the correct response.
There's another one in "Let This Be Your Last Battlefield". One of the aliens of the week is set up as someone who's hotheaded and difficult but ultimately at least somewhat sympathetic. Viewers get a hint of that second half coming when in his first exchange with Kirk and McCoy, after reacting very angrily to their (perfectly accurate) accusation that he had stolen a Federation ship, the alien visibly pulled himself together enough to thank them quite sincerely for rescuing him.
In Friends, the episode after Ross and Rachel break up (that is, the first time they broke up), Ross helps the others out after they get stuck on the road with no gas, and gets a rather reluctant 'thank you' from Rachel before they go.
Buffy the Vampire Slayer: Buffy to Spike at the end of "Intervention". She's understandably squicked out by his possession of a sex doll in her likeness, but after tromping all over his attempt to justify it, she follows up with:
"That ... thing, it ... it wasn't even real. What you did, for me, and Dawn ... that was real. I won't forget it."
This happens in Misfits when Nathan gets rescued from a totally ridiculous situation by Kelly. He doesn't actually utter the words "thank you", but he mumbles and gestures awkwardly until Kelly asks if he's trying to thank her, and he admits: "I guess I am". Cue awkward silence rife with UST.
A subversion occurs That '70s Show when Red "thanks" his son Eric for staying at home to help support the family instead of going to college after Red had a heart attack and couldn't work for a while. He expresses it by ordering Eric to go out and mow the lawn, awkwardly adding that the "lawn...thanks you for staying home." Red legitimately appreciates Eric's helping to pay the bills, but he's just extremely uncomfortable expressing his emotions except for when he's angry.
Super Robot Wars Original Generation Gaiden had this after Axel had saved Lamia, even though he was formerly an adversary (but got a Heel-Face Turn). And then the next time they meet, they help out each other and just before Axel could leave, Lamia stopped him with
Lamia: Before you leave, can I say something, Captain?
Axel: Sure. Go ahead.
Lamia: ... Thank you.
Strangely enough, an inversion shows up in Mega Man: Maverick Hunter X. After the intro stage where Zero saves X, Zero starts to walk away, but X stops him to say thanks. Zero ignores him, apparently uncomfortable with the implication, and literally jets off.
Tales of Hearts. Hisui's been at odds with Shing the entire game, owing to a solid string of misunderstandings involving Shing and his sister Kohak. When Shing pulls a dangerous Big Damn Heroes and saves Kohak atop a rumbling mountain, Hisui berates him, but calls him "Shing you idiot!" in the process. When Shing points this out, Hisui cracks: "S-so what about it? ..but I guess it's true that you did save Kohak. I'll say it once: Tha, thanks."
Knights of the Old Republic: You can get Bastila to apologize for her earlier rudeness, but according to the text it sounds like 'pulling teeth'.
Star Fox 64 has this in a few of Falco's comments, such as "I guess I should be thankful."
In Hyperdimension Neptunia, at the conclusion of the Lastation Tech Expo story arc, Neptune faces off against a giant Killer Robot out to destroy her. When she defeats it, CPU Black Heart arrives on the scene, telling her things wouldn't have come to this if she (Black Heart) hadn't been so negligent, while also having another of her tsundere moments when she actually goes to thank Neptune for her help.
And, after a very large falling out, they reconcile when Voluptua ends up thanking Jean for helping save her life.
In At Arm's Length, Kaige rescues the dragon-loathing adventurer Ginger from a monster during "Games Monsters Play". Later that evening during an uncomfortably silent moment between the two, Ginger thanks him.
In Homestuck, after John's Dad takes Jack's hat, sets it on fire, and sprays shaving cream all over it before stomping it to oblivion, Jack allows him to leave. He really hated that hat.
Wyn from the web fiction serial Dimension Heroes finds himself being saved several times throughout the course of the first book. Not one to look down on their kind acts but unwilling to change his stance of joining them, he simply says "Thank you" and continues on his way.
There's an episode which featured an opponent whom Batman feared could actually defeat him in combat (though he wouldn't admit it); when the final showdown occurs, he's in Bruce Wayne disguise and can't fight up to his full potential... until Robin comes along and "removes" the sole witness. In the denouement a day later, Batman thanks Robin for his assistance, and admits that defeating the bad guy might have been highly difficult, "maybe impossible".
In another episode, Harvey Bullock is targeted by a killer and asks Batman for help. Bullock continues to express his dislike of Batman but does thank him in the end.
Subverted in the Earthworm Jim cartoon. Jim saves the life of Bob the Killer Goldfish, who says "I don't know how to say this but... you saved my life. Thank you." He then states that he does know how to say that Jim's actions are also directly responsible for the fact that the universe is about to be destroyed.
In The Mask: The Animated Series "The Terrible Twos", The Mask rescues Lt. Kellaway from Putty Thing. Kellaway thanks him for saving his life and grudgingly admits he may not be "such a bad guy after all". The Mask then gives him a wedgie, as usual.
Subverted on Camp Lazlo: Lazlo has just saved Edward from having to blow up his favorite doll. Edward is his usual angry self, but as he walks off, he says, "Oh...and Lazlo? Tha—clean up this mess, you loser!" How sweet.
Transformers Animated: Sentinel Prime, after having been targeted by the Headmaster and reunited with his body, thanks his rival, Optimus Prime.
Optimus Prime: Wow. That must have hurt.
Sentinel Prime: More than you know.
In She-Ra: Princess of Power, Hordak gives a variant after seeing She-Ra risk her life to save the both of them from Another Dimension. They return just before a battle breaks out between the Horde and the Rebels, and Hordak commands the Horde to stand down, stating he doesn't want to owe She-Ra later for saving his life.