Aldnoah.Zero: Slaine Troyard's thoughts on Princess Asseylum are all but stated to be this, specially since she saved his life and then his father's years ago and therefore he has developed one heck of an Undying Loyalty towards her. On the other hand, in the second season it looks like Asseylum's Body Double and half-sister Lemrina is developing one on him, which is further confirmed when she first kisses him on the lips, and in a later episode (under the disguise of Asseylum) declares that they are to be engaged to marry.
While more of personal medics than bodyguards, all the significant Unemezoku in Arata: The Legend (Kotoha, Rami, and Miyabi) seem to be devoted to their masters (Arata, Mikusa, and Kadowaki, respectively) more than the call of duty requires.
Basilisk has two characters behaving like this: Chikuma Koushirou for the Iga Tsubagakure, Kagerou for the Kouga Manjidani. Both of them have feelings for their leaders, Princess Iga-no-Oboro and Koga Gennosuke respectively.
In the second season of the Black Butler anime, Claude towards Alois. His catchphrase can be interpreted roughly as "I want nothing but to deeply desire my master." Cue fangirl squee. It's subverted when Claude cruelly kills Alois himself, giving the psychotic kiddo an Alas, Poor Villain demise.
Ginji Matsuzaki's loyalties are all for Yukio Washimine, and it's almost a sure thing that they're romantically-inspired. Rock tells Yukio that he's sure she accepted the role of Yakuza boss to be with Ginji, who could never have a normal life with her. It ends tragically, however: with the Washimine clan decimated, Ginji slain by Revy, and Yukio commiting jigai with his katana right after his death.
In that same arc, one can also make the argument that Revy applies to this for Rock since this is one of the parts where the Ship Tease between them is at its most visible.
By the time the Baile de la Muerte arc finishes, Garcia has developed a HUGE one on his much older Ninja Maid Roberta. In the manga, he even kisses her.
Soi Fong developed this towards her former commander Shihoin Yoruichi after entering the omnitsukido. She worships Yoruichi as a goddess.
From the time they were very small children, Kanae Katagiri was a devoted servant and bodyguard to Uryuu's father, Ryuuken. Her feelings weren't one-sided; she's Uryuu's mother.
Blood+: All chiropteran chevaliar are hardwired to be this for their respective queen. That said, some love their queens much more than the others.
Haji takes the cake for having loved and protected Saya since he was young and still human. Not only does Haji feel nothing but love and loyalty for his master Saya, he's at it for upwards of 100 years before she even notices.
James lives only to make Diva happy and make others bow down to her. He is the only one of her chevalier to never express affection for Saya or attempt to use Diva to achieve his own ends. When Diva rejects a newly healed James, he goes full blown Yandere against the newest object to catch her eye.
Melan initially protects Marin simply because it is his duty. As time goes on, the pair begin to have feelings for one another, though their personalities (Marin is warm and loving towards many people, and Melan is gentle and soft-spoken) make it a little hard to pinpoint exactly when they start seeing each other in this light. In any case, the result is that Melan grows to love Marin so much that he continues to protect her even when it turns out she's not the person he was supposed to protect in the first place.
Chobits: This seems to happen between the female guard/firewall Dita and the male charge/database Zima at the end of the anime. Seemingly caused by Chii granting all persocoms the ability to feel emotions. In the manga their relationship is a bit more defined. The only reason Dyta is not cuddling up with Zima is because persocoms cannot really feel emotions, so they cannot love each other even if they're in love.
Gender-flipped with Kallen and Lelouch. Ace Pilot and Action Girl Kallen Kouzuki develops a crush on rebel leader Zero (who eventually does make her his bodyguard). The second season plays with this as, now knowing Zero's real identity as her classmate Lelouch Lamperouge, Kallen has a hard time reconciling her feelings for him with the Rich Idiot With No Day Job image he's projected at school. The twist? Had Lelouch let Kallen in on The Plan, she not only would have turned against the Black Knights and the rest of the world for him (as well as abandoned a Happily Ever After ending with her mother), but she would have also followed him in death. This in turn makes the ending even more bittersweet, especially during The Miraculous Birthday in which Kallen states she'll never forget (i.e. stop loving) Lelouch, even if she wanted to.
Li Xingke acted as a servant for Empress Tianzi. His crush is strong enough that Shirley persuaded Lelouch it would be criminal to separate them. He might be the "reason" why she can't marry. It's better him then the guy she was going to marry who was 40 and a Britannia Prince
Sir Gilbert Guilford and Princess Cornelia have a lot of subtext that points toward this. In fact, Guilford is such a Cornelia fanboy that he has a Cornelia collector's plate.
The only bodyguard who does not have a crush on his charge is Knight of One Bismark for Emperor Charles, and even they are pretty chummy.
In Corrector Yui, it's very strongly implied that sometimes before returning to his original identity, War Wolf aka Corrector Synchro began to fall in love with Yui. It was that one of the triggers that made him eventually return to his former self. Later, when forcibly turned back into Wolf thanks to a certain Virus, he proves to be loyal to her and even if she still bothers him with an Affectionate Nickname, he can't be mad at her just because of that.
Dragon's Reign subverts this trope because the Big Bad is revealed to be the princess, who has gone through a succession of Bodyguard Romances, each time convincing her new protector that the previous one was a villain who kept her imprisoned and took advantage of her. The hero even figures this out, but is still all but powerless against her Magnificent Bastard charms.
El Cazador de la Bruja Nadie is tasked with protecting Ellis, and ends up developing feelings for her, although it is Ellis who takes the initiative.
The Familiar of Zero combines this trope with Happiness in Slavery in regards to Saito's relationship with Louise. As her familiar, he has incentive to protect her. Eventually, he becomes her husband.
Genders are inverted where the female Lieutenant Riza Hawkeye acts as aide/right-hand woman/bodyguard to male Colonel Roy Mustang. It becomes progressively clearer throughout the manga and Brotherhood anime that their feelings for each other run much deeper than allowable by the military's anti-fraternization law (a fact that the bad guys gleefully exploit twice); it's eventually revealed that their relationship goes back to a long time before either of them joined the military since her dad was his Alchemy teacher. It's not an exaggeration to say that the most dangerous place in Amestris is between the two of them. Apparently, Word of God states that they have "marriage-worthy" mutual feelings but, as said above, the anti-fraternization rules will technically keep them apart for some time.
Lan Fan, the female bodyguard of Prince Ling Yao of Xing, has a very similar relationship with her lord. To the extent that Greed becomes a Shipper on Deck.
Mobile Suit Gundam SEED Destiny: A foregone conclusion with Athrun and Cagalli in the first part as they were both interested in each other well before he became her bodyguard. Many cute moments ensue, as he became her bodyguard because of the fact that they were interested in one another. However, they break-up midway through the series since Cagalli's ultimate priorities are rebuilding the kingdom of Orb and helping stop the war. Not every hope is lost, however, since both are more or less single at the Grand Finale (though Athrun has Meyrin, who Cagalli personally asked to keep an eye on him, as another possible suitor).
Mobile Suit Gundam Wing has a Genderflipped example: Rebellious Princess Relena, the one being protected, is obviously in love with her bodyguard of sorts Heero Yuy. He shows only a couple of outward signs that he reciprocates, but it's very subtle. There's even an odd twist on it in the second episode, where Relena protects Heero in spite of the fact that he was about to shoot her; this might even mark the point where he starts feeling something for her. Making it odder still, the attacker is fellow Gundam Pilot Duo Maxwell, who shot Heero to save Relena and is greatly confused when she chews him out and bandages the guy who was about to shoot her: "Man, when did I become the bad guy in all this?"
In After War Gundam X, after a rather rocky beginning, Garrod Ran becomes Tiffa Addil's devoted protector. He's soon crushing quite a bit on her and, despite being terrified of people due to her past, she places her trust on him and loves him back just as much. It even gets lampshaded by Tiffa's Parental Substitute/Garrod's mentor Jamil, who once "punishes" Garrod by telling him he shall stay by her side.
In Hajime no Ippo, coach Kamogawa had a female friend named Yuki, whom he and their common friend Nekota protected from the advances of stationed American soldiers. Yuki was hinted to be in love with him, but as a survivor of the nuclear bombings, she died of radiation poisoning some time later.
The Melancholy of Haruhi Suzumiya: Itsuki and Mikuru take these roles in the club's home-made movie. Mikuru's character is supposed to protect Itsuki's from Yuki, the antagonist. Given that Haruhi is directing this movie, it quickly goes pear shaped.
Hayate the Combat Butler: The entire plot of this parody series is based on this trope. It is played as many ways and as long as humanly possible. The real crush is the one the girl has for the guard but she thinks he has a crush on her, which is how she developed her crush in the first place.
Hellsing's Alucard is intensely devoted to his Master and Countess Integra Hellsing to the point of any insult done towards her in his presence triggers a Berserk Button. He's referred as her lapdog and bodyguard a couple of times, so fits this role.
Hungary: I have 100.000 soldiers! I'll fight alongside you! :D
In Hime-sama Goyojin, Adron, a hired assassin sent to steal Himeko's crown, masquerades as her bodyguard in order to get closer to her and kill her. Things get complicated when Adron develops a crush on her, and everytime he tries to murder her, he freezes up completely.
Played with in Ikki Tousen Great Guardians, where Kan'u has become a sort-of Covert Pervert for Ryuubi. (To be fair, Kan'u already felt that way from quite a while and her feelings are enhanced by a certain MacGuffin). Also, Koukin feels similarly towards Hakufu, his cousin (Funniest thing, Hakufu's mom Goei sorta encourages said crush). And yep, they sorta did bond in regards to their common feelings in Dragon Destiny.
Inu × Boku SS: Soushi makes it clear from the get-go how wonderful he thinks his mistress Ririchiyo is and that he'd willingly do anything for her. The reason he became Ririchiyo's bodyguard in the first place was because he'd fallen in love with her after she unwittingly saved him emotionally when she was a young child, and he wanted nothing more than to protect her and be as close to her as he possibly could. This desire is so strong it treads into stalker territory.
The dog Rino of Inumimi was taken in by Yuichiro's father before the events of the story. As an antisocial doberman, she served as the family security system for quite some time. It's implied throughout the series that after she went animorphic she started having feelings for him.
A serious case of Les Yay between Valmet and Koko from Jormungand. While most of it originates from Valmet, Koko not only seems to not mind, she also returns the advances, though if nothing has happened yet (officially).
The whole premise of Katanagatari is that Togame wants her bodyguard and human sword Shichika to fall in love with her so that he will develop Undying Loyalty for their quest. Shichika agrees, and the feeling eventually becomes mutual.
Played with in Kure-nai, where 7-year-old Murasaki seems to develop a puppy-love crush on her hired bodyguard/protector, Shinkurou. The relationship develops into the affectionate sort one might expect between a little sister and a caring older brother, quite unlike her REAL older brother....
In the oneshot Kuroneko Guardian the protagonist falls for his bodyguard. In the ending he outright tells her he plans on making her fall in love with him, which backfires.
Conrad Weller might feel something like this for his charge, the king Yuuri Shibuya, in Kyo Kara Maoh!.
Lupin III: The Woman Called Fujiko Mine: During the second episode, Jigen is ordered to protect Cicciolina by his boss, despite Jigen's attempts at refusal, because the boss wants his wife protected. Cicciolina develops a crush on Jigen, and manipulates him into awkward situations such as having sex in a casket.
Madlax The titular heroine, Madlax, appears to have romantic feelings for her client, Vanessa. Too bad Vanessa gets caught in Madlax's deals and is ultimately killed.
Magic Knight Rayearth gives us one truly heartwretching example. The high-ranked sorcerer Zagato is chosen as the bodyguard of Princess Emeraude, the Pillar of Cephiro, and he falls for her. It turns out she loves him back... but a Pillar isn't allowed to care for anything except for Cephiro's well-being, or the whole world will collapse. So Emeraude tries to get the Magic Knights to kill her so she can be free and pass the torch to a new Pillar; Zagato will have nothing of it, though, and in despair he kidnaps Emeraude so the Knights can't kill her, becoming the Big Bad that Hikaru, Umi and Fuu must beat...
Shizuru Viola's feelings towards Natsuki Kruger definitely fall under this (she works as both her bodyguard and assistant, and they share living quarters on campus), though she tries not to let it interfere too much with her sense of professionalism. (And she's also kinda fond of flirting with other girls, sometimes.)
Takumi and Akira are in the same sort of situation, where Takumi is the prince of Zipang and Akira is his bodyguard.
Maiden Rose: Klaus von Wolfenstein has a relationship with Taki Reizen can be seen as this. Klaus often bows down to Taki, and has expressed his desire to serve him and protect the country with him.
In Mirage of Blaze, Naoe is madly in love with his lord and master, Kagetora. Kagetora shows no sign of reciprocating, and in fact has been known to use that to keep Naoe chained to his side. Of course, this situation is exasperated by the fact that they have been reincarnated into this situation for the past 400 years. It's no wonder Naoe is losing it.
Martin initially dislikes Eva, who he is supposed to protect, but later develops feelings for her just before she is about to be finished off. Martin then tells her to meet him at a train station, but he doesn't make it.
In the main storyline, Chojuro's feelings for the 5th Mizukage go beyond simple protectiveness.
Naruto himself inverts this and plays this straight:
Inverted - It has been hinted that various Filler characters Naruto was assigned to protect developed feelings for him.
Played Straight - In The Last: Naruto the Movie, after Hanabi Hyuga is abducted and her older sister Hinata barely escapes, a task force is gathered to retrieve Hanabi; Naruto is a part of said group and additionally is tasked with protecting Hinata in case Hanabi's kidnapper goes after her again. Hinata is already in love with him, and as they spend more time together, Naruto realizes he has more personal reasons to keep her safe. They later become a Battle Couple, begin their romantic relationship, and get Happily Married.
Ash's Charizard in Pokémon, as seen in the episode Great Bowls of Fire, is this with Liza's Charizard Charla, the same Charizard who has easily thrashed him in their first meeting. But now he has wooed her and is now her bodyguard.◊ It's explicitly stated their relationship is this.
Diamond harbors feelings for Lady Berlitz/Platinum in Pokémon Adventures. He and Pearl were became her bodyguards when she became a trainer.
Powerpuff Girls Z had an episode where an actor from a superhero TV show ended up as the mayor of the city for the day. The Powerpuff Girls were assigned to be his bodyguards, with one of them quite infatuated with him.
Seiya is honor-bound to protect Saori, who's the reincarnation of Athena. He quickly develops feelings for her, and she seems to like him back too, but their relationship barely evolves at all until the Tenkai-Hen movie.
Out of the other Bronze Knights, Unicorn Jabu also has feelings for Saori, and in fact right as he's being defeated by Shun in the Tournament, he cannot stop thinking of her.
The filler Asgard saga has Siegfried, the strongest of the Asgard warriors, who is all but stated to have fallen in love with the priestess/representative of Odin on Earth, Polaris Hilda.
If the prequel Saint Seiya: The Lost Canvas counts, this is all but stated to be what Sagittarius Sisyphus actually feels for Sasha aka the Athena incarnation of the 18th century.
Inverted in Samurai Champloo, Fuu seemed to feel this way towards both her bodyguards Mugen and Jin.
Samurai Deeper Kyo has a few (Saizo for Yukimura, and arguably Hishigi for Fubuki), but Kyo's for Yuya is absolutely legendary and a little bit scary at times.
In Samurai 7, Kirara is given to this, though the person turns out to be the least expected. Her sister falls for this trope as well. It ends badly for both sisters—Kirara's crush is forever unrequited, and while Komachi's is possibly requited, the guy dies in the final episode.
The first season of Shakugan no Shana is driven by a gender-inverted version of this trope. Since Shana is possibly the biggest tsundere of all time, she doesn't admit it until the final episode and Yuji doesn't hear it, so the writers get to keep running with this trope well into season 2!
This is the basis of Shinobi Life. Kagetora is a ninja assigned to protect the princess of feudal Japan, and falls in love with her. Then he gets warped to the future by accident and ends up falling in love with the princess' descendant. Honor Before Reason abounds.
Inverted in Slayers: during the NEXT season, when Gourry is taken away from her, Lina suddenly realizes she's fallen in love with her bodyguard and companion Gourry, much to her initial surprise and dismay. Gourry has feelings for her too, but he's a lot more comfortable with them than the volatile sorceress. In fact, Gourry is the one who makes the first move, when he lectures Lina after she fakes her death without telling him. He first calls her "unsensitive", then asks if she knows what he's come to feel for her, which makes Linavery flustered.
Gender-flipped version in Sumomomo Momomo. Sanae is the heir of the Nakajima family, which has traditionally functioned as the bodyguards of the Inuzuka family. She has a huge crush on Koushi, the heir of the Inuzuka family, who she will one day have to protect from the shadows, as tradition dictates.
Sweet Ninja Girl Azuki: The format is Gender flipped , with Azuki developing the crush on him even before she becomes his bodyguard. Also notable that the feeling is definitely not reciprocated.
Time Stranger Kyoko: Both of Kyoko's bodyguards are in love with her. One of them has his feelings reciprocated, the other doesn't.
Vampire Princess Miyu: Larva was at first defeated by Miyu and bound to be her servant as a punishment, but as years passed and he followed her around in her Dark Magical Girl mission, he developed feelings for her. From Miyu's part, Larva is her Only Friend and she's very, very protective of him.
Hak from Yona of the Dawn is a classic example for Yona, though in his case the crush came before he was her bodyguard. Some of the dragons are shaping up to be this to her too.
Yu-Gi-Oh!: Anzu Mazaki and Yami Yugi from the first manga series - their initial meeting has him possessing Yugi in order to rescue her and disappearing just as quickly, leading to her developing a crush on him. He rescues her a second time in a later chapter, creating the impression on her that he was her protector. When she begins to realise that her crush is in fact a form of Yugi, she deliberately invokes the trope by putting herself in danger to bring him out. This dynamic fades later on, when he becomes his own person and gains a more equal standing as the friend and not just the vengeful protector of Yugi's companions.
Yu-Gi-Oh! GX: Juudai and Yubel have a variation on this, since she was transformed into a dragon in order to protect him, and he pledged his eternal love to her after that.
In Vampire Game Princess Ishtar has been in love with bodyguard Darres pretty much since the age of five, whereas he's never seen her as anything other than the cute kid he's in charge of babysitting...for much of the series, the only part that changes is whether he'd still use the word 'cute'.
Vampire Knight: Well, yes. Zero is used as Yuuki's "shield" by Kaname, and he falls for her, so...