In a game that prides itself on Ho Yay, Sengoku Basara gives us a little Magoichi/Mistunari ship tease in 3 if you choose (while playing as Magoichi) to side with Mitsunari. Magoichi actually treats Mitsunari's lack of social skills with snark and tends to always engage him in conversation. Mitsunari as a result acts less deranged, angsty and starts answering in words other than threats. When Magoichi asks him why he wants to keep a mercenary group like the Saika he replies : "When you joined the Toyotomi army you became a part of its treasure. There's nothing wrong with a man keeping his treasures to himself" leaving her speechless (at which she comments on his Hidden Depths when he's out of earshot). After killing Ieyasu, Mitsunari walks up to her and demands (in a rather casual way instead of his usual tone of seething rage) "Remake the deal." which can be taken as his way of saying "Don't leave me." and attacks her (the first time she blocked. Here she merely stands still) and stops the blade at her throat and removes it before walking away saying "We have much to do." As he walks away, Magoichi gently (for her) smiles before doing what he asked.
Tales of Symphonia's creators probably knew that that shipping was inevitable, so they made Relationship Values lead to Multiple Endings. Despite this, there are still scenes that favour the two main female leads more than the others; with the most blatant example being a skit that occurs in Welgaia between Lloyd and Sheena. When someone other than Colette or Sheena is your closest party member, the cutscenes are generally nonromantic, exploring various other types of relationships such as admiration and friendship; but a lot of people seemed to think they were all love options. In the sequel, the Raine and Presea options are promoted to full romantic levels.
It helps that Presea looks like a young girl around Genis' age (but is actually a woman who is a decade older than Lloyd), and Raine is Lloyd's teacher. The Genis/Presea and Regal/Presea ships often get teased; when Zelos suggests that Presea could fall in love with a much older man around Regal's age, Genis gets very defensive.
A lot of people also consider Zelos the closest thing this game has to a Gay Option due to how...friendly he is with Lloyd. Overall, Zelos seems to be the most shipped character, being paired off with everyone, male or female.
Tales of Graces has Asbel and Sophie. Seven years before the game's events, they start by vowing to protect each other. Then after they reunite seven years later, there is a scene that has Asbel kneeling in front of Sophie, letting out his regrets for his failing her. Then, after Sophie regained her memories they have a date have a little chit-chat at the place where they first met. And remember the 125th entry of The Grand List of Console Role Playing Game Clichés, "If any character in the game ever meets any other character standing alone at night looking at the moon, those two will eventually fall in love"? Despite this, Asbel still ends up with Cheria, his childhood friend. this is justified because Sophie is not human.Doesn't stop the shippers, though.
This isn't half as bad as what the cruel, cruel writing team does with potential Beta Couple Hubert and Pascal. In the original game Hubert's crush on Pascal is mostly just implied in some skits, but in Lineage and Legacies they turn it Up to Eleven. It's outright stated that Hubert is in love with her, and that's the reason he won't marry the president of Strahta's daughter. Richard and Malik are constant shippers on deck and tease Hubert about his crush ceaselessly. There's a half-dozen scenes where Hubert goes out of his way to shield Pascal from attacks. It's even implied by Fourier that Pascal might reciprocate his feelings, though she seems somewhat unaware of them. It gets to the point where Hubert outright confesses to Pascal, "my every waking thought is consumed by you." AND THEN the game yanks it away at the last minute with a Maybe Ever After.God damnit, Namco.
Up to Super Robot Wars Original Generation 2, most people think that Axel Almer and Lamia Loveless could never get along, as almost every appearance they have, they're usually enemies/rivals. The sequel Original Generation Gaiden gives them a chance to fight under one banner, and gives them a subplot that might have linked them together romantically, where the latter feels indebted to the former for saving her life. The end of the story adds Axel, in attempt to find his own paradise (on Lamia's suggestion), promises to tell her first if he ever finds one. Awww...!
The game adds up the teasing about pairing him and Einst Alfimi. There has been a lot of older men/little girl fan pairings in SRW, and both of them traveling together in Original Generation Gaiden all the time attracted the attention of lolicon fans, viewing them as a pair (it helps that Alfimi just happens to be a clone of Excellen Browning, the Alternate Universe counterpart of Axel's deceased lover Lemon Browning, who also happened to have built Lamia). It's also supported with the way she states before their departure: "I may be the only one who understands him".
Ragna is teased with both Noel and Rachel. He also has some teasing with Taokaka a little, but she seems too dumb to understand, so their relationship is more platonic so far. He was also shipped with Caelica, but then he went and died. Oh well, it still counts.
Litchi is teased between Bang and Arakune (and despite everyone else thinking that the latter is more closer to Official Couple, the game has been rather vague on her romantic feelings on him so it counts). And occasionally Carl.
Disgaea: Hour of Darkness has a bit of this between Laharl and Etna. Especially if you read Etna's journal where it's implied that her crush on the King has at least partially transferred to his son.
Also teased is Laharl and Flonne, though whether all the talk of love ever moves into romantic love or not is left up in the air. Still, considering that he was willing to sacrifice his lifeto bring her back to life, it would be hard not to believe that there is something between them.
Though Fuka herself is also teased with Valvatorez, though it was seemingly sunk when she became a Shipper on Deck. However her Epilogue with him implied she was still interested in him but did not want to "break the friendship rule."
In WarCraft, the strong alliance between Thrall and Jaina Proudmoore has raised some... interesting stuff going on between those two. The White Gnomeregan Punch Card also contains "Thrall and Jaina sitting in a tree, K-I-S-S-I-N-G." (in binary, but still), and Jaina happens to resemble Thrall's Dead Surrogate Big Sister Taretha from Lord of the Clans. World of Warcraft even gives them nearly identical character models.
Jaina: [sniffle] It was nothing, your Majesty...Just..I'm proud of my king.
It helps that he grew up as the best friend/near-brother of her only past lover and retains a lot of similarities, while she looks scarily like his dead wife and acts as a sort of surrogate mother to his son.
Kingdom Hearts II. Full stop. Hilarious given that it's a No Hugging, No Kissing game - Nomura (and Nojima) are screwing with us all, and the shipper wars they have given birth to are incredible to behold.
Final Fantasy VII's first disc is full of all sorts of Ship Tease, including a micro-dating sim where one of the three girls (and Barret) can go on a date with Cloud. Excellent examples are Cloud's and Tifa's promise under the stars scene in the beginning of the game, the Bodyguard for a Date deal, Cait Sith's 'love prediction' about Cloud and Aerith's happy future together just before she leaves your party and is killed by Sephiroth, and Yuffie kissing Cloud during the Gondola ride. It even has instances of Ship Tease with random male characters, like Mukki, Don Corneo, and the ability to date party member Barret.
Depending on your affection rating, you can have Tidus outright tell Lulu or Rikku that he would rather have them in Guadosalam. Rikku will get a little weirded out (which makes sense given she and Tidus are Like Brother and Sister) while Lulu simply says "hmm, I could add you to my list".
Lulu gets teased with Wakka quite a bit since she used to date his brother. Then come the sequel, they're an Official Couple with a baby on the way.
Rikku also gets a Ship Tease with Gippal in X-2. An optional conversation has him saying the two "were quite the couple", though Rikku denies it. However she shows plenty of signs throughout the game such as ordering everyone to go and rescue him. The two are also seen leaving the Farplane together at the end.
It's subtle, but there is a little shipteasing between Balthier and Fran in Final Fantasy XII Revenant Wings. When Tomas is trying to woo Fran, she mentions that Balthier's methods were different. You might also count the scene in the Pharos when the Sun Cryst explodes from the original game as rather shippy. Balthier's lines regarding Fran always have some kind of sexual undertone to them (but hey, don't all his lines?)
Balthier: No one knows men like Fran does.
Balthier: I always knew Fran didn't take well to being tied up. I just never knew how much. How about you?
Ashe and Basch is also plausible. In the ending, Penelo writes to Larsa, and she tells him how she hopes Basch will see Ashe because she thinks Ashe misses him (which Basch reads after Larsa hands him the letter).
In Dissidia 012 Final Fantasy, a series of scenes involves Firion trying to approach Lightning to talk to her, only for a string of Moment Killers to scare him off. It turns out he lost his rose and she found it, and he's trying to ask for it back but is embarrassed about the Hot-Blooded rebel having to ask the resident Action Girl for his flower (in his exact words, "a grown man asking for his flower back..."). However, the subtext is very thin, and is complete with Cecil appointing himself Firion's wingman.
Cecil: "You were staring at Light. Is it about her?"
Firion: "No, not exactly. I..."
Cecil: "Too shy to start a conversation?"
Firion: "This has nothing to do with being shy!"
Firion: "No, don't call her over!"
And then when he finally does get to talk to her, the Ship Tease still goes strong as Lightning returns it to him and notes that for both of them, the sight of that rose is the key to their memories, and asks him to keep it safe because when he remembers everything, she might need it back for help with the same.
Terra gets ship teases with Onion Knight, Cloud and Vaan. Vaan and Onion Knight appoint themselves her protectors, worrying about her safety and councilling her on following her heart to find out what she truly wants. Cloud meanwhile waxes poetic with her about their dreams for the future in spite of their self-doubts.
The Legend of Zelda: Twilight Princess did its share of Ship Teasing. Between the little come-back-safely speech Ilia gives to Link (complete with appropriate music swelling in the background), the hand-holding scene between Link and Zelda before the final battle, and the heartstring-tugging farewell by Midna in which she almost says something emotional to Link, the shippers had a field day...especially considering that Link's a Heroic Mime with no dialogue to offer clues.
There tends to be an underlying vibe to any scene with Link and Zelda in it, and he's shown (and implied via dialogue) to be quite motivated to protect her. In particular, there's a great deal of unspoken emotion in their last scene together, to be interpreted as the player wills.
Solid Snake's codec transmissions regarding Samus Aran in Super Smash Bros. Brawl could be regarded as a form of Ship Tease, since it's all one-sided and we have no way of knowing how Samus feels about the matter. That hasn't stopped them from becoming the game's resident One True Pairing...though the pairing's support has less to do with any perceived teasing and more to do with how their combined sex appeal is dense enough to create a singularity.
Interestingly enough, Gears of War 2 has some of this between Marcus and Anya, such as the way Anya asks him to take care of himself when he descends into the Hollow, and Marcus calling repeatedly over the radio at the end to see if Anya is okay, and looking extremely relieved when he spots her on the next Raven helicopter.
The first game kind of hinted at an old relationship when they meet up briefly at the start of the game. You never saw her again, so nothing more came of it.
Paper Mario: The Thousand-Year Door features Mario getting kissed by each of his female party members (we're assuming that Vivian is female) and no less than four times by Ms. Mowz (which makes Goombella jealous).note Ms. Mowz can also learn a special skill that allows her to kiss Mario at any time for HP recovery.Vivian almost makes a love confession to Mario in the ending, but decides that he and Peach would be a good couple, and Goombella is about to tell Mario something she hadn't been able to express to him before in her last email, but decides to save it for later. Peach has an almost romantic bond with TEC, especially when educating him about human feelings, and by the time Grodus has him deleted for helping her get classified information for Mario, he declares his love for her just before shutting down (he gets better).
Super Paper Mario is a gigantic ship tease for Bowser/Peach fans. They get married in the opening and Bowser constantly declares his love for her throughout the game. Then there's the scene near the end where Bowser stays behind to hold up the ceiling, Peach stays a little longer than Mario and Luigi, and later on falls on top of him offscreen. Considering Bowser is covered in spikes, he probably caught her in his arms or on his chest. Their marriage is never really annulled either.
After Heavy/Medic grew to prominence amongst Team Fortress 2 fans, hints about their relationship began to be sprinkled about the various supplementary material, such as the Sniper's "Beaux and Arrows" achievement (kill a Heavy/Medic pair) and their strangely intimate interactions during open-heart surgery in the "Meet the Medic" video. Though, the WAR update attempted to torpedo it with the Demoman's Medic-specific taunt that suggests the Medic is married.
Spy/Sniper fans take some of their domination taunts and achievements as ship teasing. But then again, this is the Spy and the Sniper.
Sniper/Medic fans take the Sniper's "charge me" voice clips as Ship Teasing.
From the sound of these (robotized) unused Domination lines, the Administrator was unsuccessful at preventing their friendship.
Prior to the 2011 Australian Christmas update, the Pyro and Engineer got a comic together.
Fire Emblem lets you control the amount of Ship Tease in your game with its support conversations. Starting with the sixth game, each character has 3-7 characters they're compatible with and some of them might lead to a Relationship Upgrade. The conversations for Support Levels C and B are the cute Ship Tease ones with 95% of the A level conversations being the actual declaration of love. Roy at first is the only one who can pair up with others and have it noted in the "Where Are They Now?" Epilogue, but later on, this system extended to beyond the main lord.
Blazing Sword goes even further with this for the Lord characters. While Eliwood, Lyn, and Hector have several romantic options each, Ninian is canonically in love with Eliwood no matter what supports you choose, and you get a special ending where she stays with him at the end. Hector, meanwhile, gets numerous scenes alone with Lyn in Hector Mode, including two special conversations towards the end that can only be unlocked if they have A support. Neither of his other two love interests get equivalent scenes, and both the unique A Support sequences play music tracks that aren't used anywhere else in the entire game.
Fire Emblem Tellius : While Path of Radiance's ending establishes no pairings (you only get a different last line from the person Ike has A support with), the system returns in Radiant Dawn. The support conversations are usually far more generic, however. But like Blazing Sword, some pairs get special conversations near the end if they have reached A support by then, them being Boyd/Mist, Sothe/Micaiah, and Ike/Soren.
Chrom and Sumia: A.) She's the only character along with Chrom, Lissa, Validar, and Lucina to appear in an animated cutscene, and B.) Both she and Chrom have a small pool of love interests (four for Sumia and five for Chrom, counting the generic village girl, and they can also get with the Avatar depending on the gender you give him/her.), while the others have a much wider pool (and the Avatar can get with anybody.)
Chrom and the Avatar: Despite how the Avatar can get with anybody of the opposite sex, s/he and Chrom are still extremely close whether they marry or not. In fact, if the Avatar is a girl and they're not married, Chrom's daughter Lucina will pretty much accuse girl!Avatar of being her dad's other woman, and when girl!Avatar says and proves that she isn't, Lucina will be flabbergasted to see she's "immune" to Chrom's "charms", and follow it via borderline demanding that girl!Avatar falls for him. On the other hand, if Chrom and girl!Avatar do marry, there's quite the emphasis on the complications born from her being Grima's Soul Jarand the person destined to kill Chrom. Even the DLC chapters seem to get on it, as in The Future Past Grima (though the Avatar's body) will taunt poor Lucina with how much the Avatar, regardless of the chosen gender and/or the Avatar's marriage, loved and adored Chrom. And in the end of the game, when the Avatar is trapped by Grima, s/he can only be brought back... by Chrom's voice.
Shiala, if she survives Mass Effect 1, comes back in the sequel and is visibly attracted to Shepard, but nothing comes out of it.
In Mass Effect 3, James Vega flirts with a female Shepard, but it never goes further than that.
Tali gets flustered around a female Shepard, but she is only a romance option for male Shepard.
Largely lampshaded with Mordin Solus in Mass Effect 2, but only if you speak to him enough times and you're either in no current romance or are loyal to one from the first game. It could be assumed this is a playful jab from the writers at those who ship their player character with everyone, but it certainly hasn't stopped people from assuming that Mordin might actually be serious about the possibility of him "trying Shepard".
In the final Mass Effect 3 DLC "Citadel", you throw a party for the crew. During the course of the party, depending on who is alive/present and your relationship status at the time, you can see: Ashley and Vega flirting with each other, EDI making extensive comments on Traynor's attraction to her voice, Shepard can comment on Jack and Miranda's Belligerent Sexual Tension, Zaeed displays a blatant crush on Samara, Shepard's own teasing with Samara can go even further, and Shepard can have a one night stand with Javik, of all people (which they will never speak of again).
As for Bishop, he'll have a few instances of jealousy over the Knight-Commander's relationship, romantic or not, with Casavir, and will offer to run away with her if she has high enough influence.
Also, Elanee/Casavir will be really jealous if you have a higher influence with Neeshka/Bishop than with them. Really jealous.
Elanee: You're spending more time with Neeshka than with me!
Casavir: I don't like how that ranger looks at you.
Some dialogue with Kaelyn in Mask of the Betrayer could potentially be interpreted as this, but not blatantly.
In Knights of the Old Republic 2, if a male player character tells Mira that they just want to get to know her better, her immediate assumption is that he wants to get her into bed. Her immediate refusal ruins it, though.
Pokémon, of all RPGs, had a ship tease, in the fourth generation. One of the villain team's commanders says, "So what is it? Are you some lovey-dovey couple to the rescue?", in a scene where you are with one of your rivals, the one that is the opposite gender's playable character.
Playing as May, the female character, in Pokémon Emerald, Brendan will state how he saw a Pokemon, Rayquaza, and wish you were there to see it with him.
The Pokémon Gold and Silver remakes, HeartGold and SoulSilver, offer two instances, one intentional and one with severely Unfortunate Implications. The intentional occasion takes place when the player reaches the day care couple for the first time and are greeted by either Gold/Ethan or Lyra (depending on player gender) after a brief conversation, their grandfather will comment about them having a crush on the player character. Naturally they'll force their grandparents to change the topic then run out in embarrassment. The unintentional instance occurs when trying to infiltrate Team Rocket's radio tower in disguise only for Silver (the rival) to run in and forcefully strip the player character. Granted he's only trying to remove the Rocket uniform since he despises the organization and can't see his rival among their ranks, still this scene alone has managed to generate hundreds of Silver/Lyra and Silver/Gold drawings.
The scene in HeartGold where resident Memetic Sex Goddess Cynthia mentions that your eyes remind her of someone from Sinnoh.
N's dialogue toward the player can be taken as very ship-teasing as well, if in a Stalker with a Crush way. This is thrown out the window at the end when N states that he by this late point 'was starting to like you', either Ship Sinking or a new start of more direct Ship Tease. Either way, by this point we've learned N probably isn't mental-emotionally mature enough for a serious relationship anyway.
Pokémon Colosseum has Eagun, an Old Master who started off with a Pikachu. His granddaughter bears a rather striking resemblence to Misty. A possible nod to the anime, perhaps?
Pokémon Ranger does this. Quite a bit, actually. For RangerShipping (Solana x Lunick) fans, you've got not only the various little hints throughout the game, you've also got the Groudon mission. Same with the Kyogre mission for Solana/Lunick x Aria fans. Guardian Signs dabbles in a bit of ObliviaShipping (Ben x Summer) too. And Shadows of Almia has a bit of VatonageShipping/RangerSchoolShipping (Kate x Keith and Kellyn x Keith) too.
Silent Hill 2 has its own expectedly horrifying contributions to the trope with James, a surly individual who travelled to the eponymous town to search for his dead wife, and Maria, an extremely flirtatious and slightly Tsundere woman who reminds James of aforementioned dead wife. For a while it seems as if the two will enter a Replacement Goldfish- esque relationship (and they do in the "Maria" ending), but turns out that not only is Maria a figment of James' imagination formed from a combination of his sexual frustration and refusal to accept his wife's death, but that she's the one who has been unleashing all the horror on James throughout the course of the game, and the Final Boss. Slap-Slap-Kiss it isn't.
Mega Man X fans have shipped X/Zero ever since its first game, citing Zero's Heroic Sacrifice for X and the latter's desire for Zero to be the one to kill him should X go rogue as proof. There's also the (optional) reunion cutscene in X6 in which X looks a bit too enthusiastic (to the point of blushing) when he sees Zero alive and well.
Mega Man Zero has various moments of Ship Tease between Zero (yes, that Zero) and Ciel (who's human, by the way), not only during the series' run, but in the accompanying materials as well. Amongst many, there's this little piece of dialogue before the end of the first game:
"Zero, I'm happy that I could meet you...if it were not for you, everyone would be gone by now...Promise me that you will come back alive. Even if you cannot destroy Neo Arcadia, I just want you to be able to return safely."
"I never cared about justice, and I don't recall ever calling myself a hero...I have always only fought for the people I believe in. I won't hesitate...If an enemy appears in front of me, I will destroy it! Ciel, believe in me!"
The entire lyric sang by Rie Tanaka, Ciel's seiyuu herself, in the song Freesia, in Remastered Rockman Zero Soundtracks PHYSIS depicts Ciel's love for Zero.
For a series that tends to avoid the topic of relationships in the games (except for Amy, who is...rather clingy and it seems one-sided), Sonic the Hedgehog has been known to ship tease a few times. Knuckles and Rouge in SA2, for starters. Then there's the end of Sonic Rush, where Sonic and Blaze have a long stare at each other and are trying to hold on to each other as long as possible before they get separated - Sonic's holding on with both hands. It's as if they're both reluctant to part ways.
And then there's Sonic Chronicles. Being a turn-based RPG by Bioware, it's hardly surprising that you can pursue optional dialogues with your various allies. Sonic/Amy is well-supported, Sonic/Rouge is hinted at if you're sarcastic with Amy, but the real tease is Knuckles/Shade towards the end. Knuckles could just be relieved that he's not the Last of His Kind anymore, but it could also be something more specific.
Resident Evil. The entire series is filled with scope for interpretation for Ship Teases, though there are a few blatant ones that should probably be listed. RE1, the scene where Jill puts her head on Chris's shoulder. RE2, Leon screaming her name when Ada "dies". RE4, Leon almost blatantly checks out Ada's ass as she's leaving the boat in the cinematic just before you begin playing the island. RE5, Jill tackling Wesker through a window to save Chris, or the fact that you get a game over if you kill Jill in the game.
Not to mention Chris was willing to stay with Jill instead of chasing after Wesker, putting the whole world in danger.
In the closing scene of RE4, Ashley all but invites Leon into her pants; he politely declines.
When playing as Chris in the first game, when you save Jill from the basement prison, they hug in an intimate manner.
Also in the fifth game, Jill's under Wesker's control. Chris sounds staggeringly pained whenever Jill is mentioned (as she seemingly died before the events of the game), and the way he acts around her after freeing her is loaded with tension.
Resident Evil: Revelations: Chris acts as though he's Married to the Job and ignores the advances of his mission partner Jessica...at least until Jill gets captured. From that point on, he plows through everyone to save her.
Resident Evil 6: the entire scenario between Sherry Birkin and newcomer Jake Muller is tension galore during their quieter scenes. There's one tidbit where they're trapped in a research facility in China; Jake has nothing but pants on, Sherry's in a skimpy hospital gown, they meet, and...
The night before the final battle, Vyse talks to both Aika and Fina and can reassure them one way or another - he can put his arm around Fina's shoulders, and if he says the right thing to Aika, she'll kiss his cheek.
On Clara's ship, Aika and Fina wake up in bed together with no apparent awkwardness at all (it's not what it sounds like, to be fair), and when they both mention him to Clara, she promptly assumes they like both him that way.
The part where Aika is holding Fina after she's badly injured on Crescent Isle, while Vyse confronts Ramirez. Or the time where Aika glomps Vyse after they're reunited in Daccat's tomb, where Fina hugs Vyse after he Aika, and Glider rescue her from Valua's palace, and where Aika glomps Fina out of sheer happiness in the ending. All of these are about as ship-teasing as the aforementioned scenes.
In their cameo appearance in Valkyria Chronicles, Vyse and Aika will call out each other's names if they're killed; also, if they're close enough to provide supporting fire, they can say things like "Let me help, Vyse baby!"
The Luminous Arc series have it as a part of the gameplay mechanics, both in and out of Intermissions between each game's protagonist and most of their female party members. In the first game, while there's not-so-subtle hints of Alph/Lucia, there's also Alph/Cecille, Leon/Cecille, Nikolai/Cecille, Heath/Iris, Alph/Vanessa (!)...
Luminous Arc 2 brings it back with two potential love interests for Roland, depending on dialogue choices, he can end up with either Althea or Fatima. Beside those two, there's Ship Teasing for Roland/Dia, Roland/Sadie, Roland/Karen...And the blatant teasing for Rasche/Dia can't be a coincidence, especially their teasing about forming their own Final Bond after seeing Roland does it with Althea or Fatima.
Luminous Arc 3's Refi can find himself in this, as well as forming a closer relationship with one of the girls for a Zodiac Card to perform a Unison Strike. For some extra, he is NOT limited to female.
Psychonauts: Sasha Nein and Milla Vodello. Despite being complete polar opposites, in-game bonuses like characters' memories and concept art hint that there might be some more going on than being just co-workers. Psychopedia seems to confirm that yes, Milla has a crush on Sasha, but whether or not he reciprocates is up for debate.
Snow Sakura has this one at the end of Kozue's route with the Bromantic Foil Sumoyoshi and your resident Tsundere Saki, who compliments him on a nice rousing speech to Kozue while blushing noticeably. There were a few fans quite disappointed with Digital Objet not doing more with it.
Lux-Pain. You can pair roughly half the cast with each other and it makes at least a little sense.
Assassin's Creed: Brotherhood teases at Lucy and Desmond. In the first game, they were simply working together, with only vague hints that she was on his side up until the end. The sequel had a little bit of ship teasing, but not a lot. By the time of Brotherhood, though, it's quite clear there's some unspoken mutual attraction there, especially in one of the out-of-Animus sequences where Desmond and Lucy have a brief, heartfelt conversation while looking up at the moon. Then there's the ending...
Soulcalibur gives us Kilik/Xianghua, numerous times over. From their Destined Battle in II (a Fighting Your Friend moment where neither wants the other to move on for fear of them dying in the battle against Soul Edge/Inferno) to their endings in III (Kilik's having him outright ask Xianghua to stay with him as they share a tender moment, Xianghua's having her hint her affections to an oblivious Kilik) as well as the two are the only characters in III to have a dual Weapons Demonstration, it's quite clear that these two are more than True Companions. Soulcalibur IV drives home their status as the Official Couple quite soundly: in Xianghua's ending, she pleads for him to not go through with his Heroic Sacrifice and confronts him on their shared sexual chemistry, Kilik painfully states that he wants to be with her, but there simply isn't a way and instead wants her to find happiness in a life without him. Right as he starts his kamikaze attempt, Xianghua runs up to Kilik and embraces him, telling him that she's going to stay with him; Kilik replies with "thank you."
This went in a very interesting direction in V, which at first implies the pairing is outright sunk: Xianghua has a daughter, and Kilik is not the father. Guess who Xiba's parents are, though.
The Harvest Moon games set in Forget-me-Not Valley have Rock with the female PC. He's one of the potential Love Interest characters for you, so what's so odd about that, you ask? The fact that the game continues to tease PC/Rock even after one or both of you get married. Rock will continue to make romantic comments toward you even after you marry someone else, and once he gets married, his wife Lumina will chew him out about it.
Although Guybrush and Elaine were already neatly paired and Happily Married, this did not stop the developers of Tales of Monkey Island from throwing some shipteasing (along with Ship Sinking) moments between Guybrush and his fangirl, Morgan Le Flay. Noticeably in The Lair of the Leviathan and Rise of the Pirate God.
The ending of Portal 2 is a parade of Ship Teasing. First, the Turret opera heavily hints that GLaDOS may actually deeply care for Chell (especially considering the English translation), further solidified by the ending song "Want You Gone", which may as well have been titled "Tsundere: The Song". Second, Chell's final scene has her reunited withCompanion Cube. Third, the very final scene has Wheatley lamenting all the bad things he did, and that all he wants to do now is apologise to Chell.
Some Chrono Trigger fans have latched on to Crono and Lucca, in large part due to Lucca being the only other character to embrace Crono in a cutscene on his revival if Marle isn't in the party.
Although the series as a whole doesn't do much in the way of ship teasing, the bonus game Professor Layton's London Life has a very subtle one that hints at the possibility of pairing the two young people in the Professor's life - his apprentice Luke and his adopted daughter Flora. It's especially hinted in the way Luke reacts rather violently to the possibility that Flora has been kidnapped.
Solatorobo teases Red x Elh enough during the main game, but the DLC quests take it Up to Eleven. In #5, they both act embarrassed when Red sees Elh in her cheerleader outfit, and she's disappointed if Red doesn't manage to beat the track record (which is the condition she agreed to in order to wear that outfit in the first place). In #7, she gets extremely upset when Red has Princess Terria and Toffee fangirling over him, and in the end Red admits he wanted to give her the tournament prize as they make up. #8 borders on "They Do with the Serial Numbers Filed Off", as it eventually turns into an Interrupted Declaration of Love. It also teases Béluga x Merveille a couple times, with him giving her a hologram of flowers and losing an arena match because he was trying to show off too much.
Shale in Dragon Age: Origins gets a telling remark about how attractive Sten's body looks in battle, while he affectionately calls her "kadan", a term that means something like "close to the heart" in the Qunari language. And then there's all of Zevran's leering at Wynne in particular and her "magical bosom".
In the Awakening expansion, despite there being no romance options, Nathaniel and Velanna's conversations contain a lot of Belligerent Sexual Tension, while Anders and a Female!Warden can engage in a fair share of flirting. Averted in the case of Oghren and Sigrun, where any Unresolved Sexual Tension is merely a figment of Oghren's booze-addled imagination.
In Dragon Age II, Bethany gets flustered around Sebastian, who happily flirts with her when not romanced, whilst Carver has a very obvious crush on Merrill. Fenris and Isabela are also revealed to have a friends with benefits relationship going when not romanced, while Aveline can be flirted with repeatedly by Hawke but it doesn't go anywhere. Hawke can even throw a couple of flirty comments Varric's way, while Varric once admits that he does consider a Female Hawke to be beautiful... but unfortunately he's not into humans.
Enslaved: Odyssey to the West, there seems to be quite a bit for Monkey and Trip, especially evident in the end of the fourth chaper where they share a rather long Held Gaze, after Trip scans the dog.
You'd think the Street Fighter series would be exempt from this trope, but the chemistry shared between series leads Ryu and Chun-Li invoke this hard. Ryu respects her abilities greatly and considers her to be a very good friend, while Chun-Li has a lot of admiration for him and enjoys fighting him every chance she gets. The fact that they're in everycrossover title together only encourages things.
IIRC, even if it doesn't come up in the games themselves there's some spin-off media (comicbooks, etc) that explicitly states they are either now, could be or had in the past been in a relationship.
There's also the fact that Sakura's Hero-Worshipper tendencies to Ryu have pretty much evolved into her having a blatant crush on him. Seriously, the girl actually refers to Ryu as "dreamy" in one of her post-fight quotes against Sagat, in The Ties that Bindshe gives him a Cooldown Hug after he almost falls victim to his Superpowered Evil Side and then stays by him when he has an Heroic BSOD because of that, and both of her endings have her either helping Ryu after he destroys BLECE (IV) or him dropping by to visit her (Super IV).
Guy and Rose get a pretty hefty dose of this in SSFIV, perhaps unintentionally. The idea behind Guy's Rival Battle with Rose is that Guy is trying to stop Rose from facing Bison, something he failed to prevent in Street Fighter Alpha 3, because he sees it as Rose being a martyr, but the romantic subtext comes on strong for anyone who's seen their fight (their banter in-battle consists of, among other lines, Guy somberly asking Rose to reconsider, Rose sorrowfully proclaiming that shedoesn'twant to die, and both fighters apologizing before unleashing their Ultras) and their linked endings (Guy becomes fiercely protective of Rose and unusually emotive when Bison abducts her, and Rose is roused back to life by Guy's concerned urging). This becomes stranger if you take into consideration that, according to Final Fight 2, Guy already has a fiancee.
Halo seems to do this between Master Chief and Cortana (even though Cortana is an AI), especially in the third game when Chief rescued Cortana from the Gravemind.
In the fourth game, Master Chief goes to extraordinary lengths to try and save Cortana when her programming begins to rapidly detoriate due to rampancy. Cortana ultimately performs a Heroic Sacrifice to save the Chief, but not before revealing her deepest desire was to be able to touch him once before she dies.
The original StarCraft had many of these between Jim Raynor and Sarah Kerrigan. From the first time they met when it was shown that Raynor had some attraction to her from the start and even to Kerrigan's mission on New Gettysburg where he tried to convince her not to undertake the mission due to the danger. The second game takes this even further with almost every character seems to refer to Kerrigan as Raynor's girlfriend in one form or another.
At one point, Serana mentions that she spent a long time slumbering with her Elder Scroll and jokes that she thought she should know more about something after sleeping with it a lot. The Dragonborn then gets the chance to suggest that Serana wants to know him/her better. She declines. Later on, when confronting Lord Harkon, a Dawnguard aligned Dragonborn can respond to Harkon's accusation that s/he would kill all vampires, including Serana, by saying that "Serana means too much to me." Harkon will remark, with an almost-defeated tone, that Serana "was lost to me the moment she accepted a mortal into her life."
This is teased to some degree in Thor: God of Thunder, a game set before the events of Thor itself, after Sif is impaled and becomes temporarily dead. Her death enrages Thor and causes him to seek vengeance, to the point where Odin worries that "Thor will slaughter and bring holocaust" if he doesn't do anything. It probably doesn't help that she died in Thor's arms either.
Odin:(discussing bringing Sif back to life and interfering with fate) If I do not, I fear that Thor will...
Loki: Thor will defy you and wage war against the Jotuns from now until Ragnarok.