In Suikoden V, while (as is typical to the series) the Official Couple for the main character is never explicitly stated, the game beats the player over the head with indirect implications of a romance between the Prince and his bodyguard Lyon. However, it's popular among fans to pair him instead with his younger sister's bodyguard Miakis, a slightly older Genki Girl who's probably the most popular character in the game (or at least the most popular female character). This is particularly true in Japan, where the volume of fanart and fanfics implies that the Prince and Miakis are preferred over the semi-Official Couple by a roughly 3 to 1 margin.
Roy/Lyon also seems to be more popular than Prince/Lyon.
A great many Tales of Legendia fans in the West prefer Senel/Chloe to the heavily implied Senel/Shirley. After all, Senel and Chloe spend most of the game getting to know one another and discovering what they have in common (though, ironically enough, their similarities are used in-game as the chief reason they can't end up together). Meanwhile, Senel introduces Shirley as his sister, was in a relationship with Shirley's actual sister, and when he spurns Shirley for her dead sister, she turns into a Woobie, Destroyer of Worlds who almost floods the world.
In Tales of the Abyss, Luke/Tear. One of the few examples in the entire Tales series where the Fan-Preferred Couple (Ho Yay pairings notwithstanding) is completely supported by the canon. In the case of side couple Peony/Nephry, Peony's canonically still pining after her even after ten years, but there's a lot more visible shipping activity for him and Jade. (Weirder still if you consider that Jade is Nephry's brother.)
Tales of Vesperia has a ludicrous amount of Rita/Raven fanart, especially on Pixiv, probably owing to their dynamic seemingly having Slap-Slap-Kiss potential.
Flynn/Yuri and Estelle/Rita have the most amount of fanwork by far on the English side of fandom, but Yuri/Judith makes a very strong showing as well.
Jade Empire has a maximum of three romantic options within the party... so, naturally, the most popular pairing is The PC/Sagacious Zu, a character who makes a Heroic Sacrifice right when the canon romances begin to play themselves out.
Not to mention he's at least twice as old as the three romantic options, seeing as he was already an adult when he killed Sun Li's wife and "kidnapped" Dawn Star, an infant at the time. By the way, Dawn Star was named for the spectacle the burning of Dirge causes.
For a time in the Mystery of the Emblem fandom, people greatly preferred Marth with Catria instead of his canon girlfriend and eventual wife Caeda/Shiida, whom they preferred to pair with Ogma. In an aversion of Die for Our Ship, they get along with Marth/Caeda fans, though.
Largely as a result of Marth Debuted in Smash Bros., Marth/Roy for Melee and Marth/Ike for Brawl are both much more popular than the canonical Marth/Caeda amongst Western fans.
For the seventh game, a surprisingly popular pairing amongst the steamy fanart crowd is Dark Action mom Sonia Reed and her Number Two, Ursula the Blue Crow. It's not hard to see why: Ursula's Undying Loyalty to Sonia combined with Sonia's Alpha Bitch personality and penchant for wearing Stripperiffic black leather lead to obvious dominant/submissive implications, and they definitely seem closer than Sonia and her canonical husband Brendan (part of this may also be due to the fact that Brendan is huge, muscular, hairy, and in his fifties, making him an unlikely choice for steamy fanart).
Fire Emblem Elibe has Erk and Priscilla, helped by the fact that this is her only romance option with a happy ending.
The Tellius sector has a large faction of fans who still wish Ike and Elincia had gotten married instead of Elincia marrying her loyal knight Geoffrey and Ike leaving the continent either alone or with Soren or Ranulf. From the 10th game, pairing Micaiah with Pelleas is preferred to the canon Sothe/Micaiah.
Fire Emblem Awakening, due to the massive amount of marriage potential, generally doesn't apply but for a couple of exceptions, mostly Basilio/Flavia and Maribelle/Lissa, both of whom have a very solid relationship in their supports and in story scenes.
Speaking of Super Smash Bros., many fans of Brawl are partial to the pairing of Solid Snake/Samus Aran. The game itself encourages the pairing through Snake's codec transmissions on Shadow Moses Island in which he talks to Otacon and Mei Ling about Samus; he says things like "Sounds like my kind of woman" and "But underneath that metal exterior beats the heart of a woman." The fact that the pairing is technically impossible outside of the Smash Bros. setting (not least because Snake doesn't even belong to Nintendo) deters pretty much no one. Before Brawl it seemed the preferred pairing was Samus and Capt. Falcon.
Since his announcement for Smash Bros 4., Little Mac/Samus has been gathering some steam.
That's all because Little Mac's reveal trailer compares the height difference between him and Samus (who is much taller). Most people would agree that Wii Fit Trainer is more fitting choice for him.
Fate/stay night is an H-game, so naturally the only canon pairings are with the main character (and, well, there's some with the villains). Even so, there are at least as many Archer/Rin fans as there are Shirou/Rin fans, if not more. Never mind that Archer is the Future Badass OF Shirou, making that pairing technically canon.
It also probably has a lot to do with the fact that Shirou has two other girls to choose from, one of whom is the main girl of the Fate route/anime (and thus the most popular pairing) or Sakura, who desperately needs him. Plus, the game (particularly UBW) strongly hints that Archer cares deeply for Rin, and the version of Shirou that does end up with Rin is the one who most closely resembles Archer of the three (although a lot more optimistic).
Jon Talbain and Felicia from Darkstalkers have appeared in more fanart than can be counted. This being said, there's not much to link them in the games, though the comics and OVA can be seen as evidence.
Demitri and Morrigan. It's not nearly at the height of Felicia/Jon, but it does have a good share of vocal supporters.
You'd be surprised at how many times the pairing of Morrigan/Felicia pops up among the fandom. Morrigan's pet names for Felicia (apparently, Morrigan still calls Felicia "kitten" according to Cross Edge, and in Marvel vs. Capcom 3, Morrigan tags out with Felicia with the call of "Kitty!") do not help in the slightest.
Donovan/Hsien-Ko was likely started due to their interactions in the anime.
Super Robot Wars generally avoids this between characters from licensed series, in hopes of preventing any unnecessary Ship to Ship Combat. However, female protagonist Setsuko Ohara of Super Robot Wars Z and Shinn Asuka in the same game is probably the most supported pairing, if not, the prime Crossover Ship in existence, as it's one of the few that actually makes a lot of sense considering their close relationship in-game.
Kairi from Kingdom Hearts is semi-offically paired with Sora (they both are shown to like the idea of sharing a Paopu fruit with each other, which is pretty much a mythical engagment-ring). Among many fangirls, however, the pairing of Sora with his best friendand rival Riku is vastly more popular.
Pairing Kairi with Riku is quite popular too since it was implied in the first one that he liked her first then Sora, (first guy wins?).
Also from BBS (more so among fans of yaoi), Ventus/Vanitas. This becomes Squicky because Ventus and Vanitas are technically the same person. However, as other pairings demonstrate, the semi-canon Xion/Roxas included, in the universe of Kingdom HeartsScrew Yourself isn't uncommon.
In Persona 2, the most popular pairings are Tatsuya/Maya and Tatsuya/Jun, with Tatsuya and Jun probably just beating out Tatsuya and Maya as the most popular pairing. The third option, Tatsuya/Lisa hardly ever has supporters.
Although Persona 4 doesn't have an official couple (thanks in part to the fact that you can date everyone), the Protagonist usually seems to end up with Naoto in fanworks, to the point that the aforementioned spoiler is practically entering It Was His Sled territory. Yukiko and Rise are in a dead heat for second, with Yukiko apparently winning by a slight margin.
Fans of the older characters in the game tend to ship Dojima/Adachi. A lot. Never mind that Adachi is the Big Bad of the game and tried to get Dojima's daughter killed. And all of this started when Adachi tried to rape two women. It's said that Adachi/Nanako has a particularly big pairing in Japan, also. Nanako is a seven year old, by the way.
Persona 3 has the option of the hero dating any girl in your party as well, but the fans overwhelmingly prefer him with Yukari, Aigis, or Elizabeth. Mitsuru/Akihiko and Mitsuru/Yukari are also very popular, more so than pairing her with the Main.
Thanks to certain Social Link events in Persona 3 Portable, Shinjiro/FeMC has been reaching this level in epic proportions. It does make a certain amount of gameplay sense, since dating him allows for you to indirectly save his life. Sort of like Zelos. Although he ends up hospitalized for the rest of the game until the senior's graduation day.
Metal Gear Solid, my god. Among the people who play this game who care about shipping, Snake/Otacon trumps Snake/Meryl (the CANON) by at least ten to one. The fact that you can actually kill off Meryl in-game to get a Ho Yayish ending with Otacon instead really doesn't help.
Snake and Meryl dated for about three weeks after Metal Gear Solid 1. After they split, Snake went off to live with Otacon, thus beginning a ten-year partnership. They even adopt a child. The vast majority of Ship Tease involving Snake is with Otacon, not Meryl, but depending on how you interpret it, they could just be living together as friends. ("You and your overactive libido," anyone?) However, Word of God has it that David Hayter, Snake's voice actor, has repeatedly gone on record saying that he and Otacon's voice actor played the two as lovers. Meryl ends up marrying Butt Monkey Johnny Sasaki.
Nearly every couple in Silent Hill is Fan Preferred, as most characters are either dead, insane, or both. The most popular seems to be Harry, the protagonist of the first game, and Lisa, the nurse he periodically encounters who attempts to help him, which was torpedoedhard near the end when Lisa discovers she was Dead All Along and becomes a permanent part of the town (or something).
Neeshka was planned to be a canon couple, but it was cut from the game due to time restraints. It's not too hard to see where they intended to take it, and it's a lot more complete than Elanee's, even though it isn't, you know, complete.
In the same vein, Bishop is also a planned but cut romance option that fans seems to prefer over Casavir, partially due to the latter reminding them of Anomen, and partially because the former has heaps of Belligerent Sexual Tension with the female protagonist and, like Neeshka, feels more "complete" than the actual complete romance.
Fans like them so much they made a mod that allows a "proper" romance, complete with an epilogue in Mask of the Betrayer.
Jaina and everyone's favorite orc, Thrall, is another popular ship. Such that Chris Metzenmercilessly sank with the recent novel having Thrall become mates with the Maghari Shamanka Aggra seemingly out of nowhere then letting Jaina get with Kalecgos in Mo P. Baring that, stated with extreme confidence that the Thrall/Jaina pairing will never happen during the Q&A at Blizzcon 2010. It didn't really help that designers had previously Lamphsaded the Thrall/Jaina pairing in an easter egg.
The designers poked fun (or just rubbed salt in the wound, depending on your view) at the Ship Sinking during Thrall and Aggra's in game wedding. After the wedding concludes, if you stick around long enough, you can catch Jaina openly sobbing.
On that note, some fans liked the idea of a Jaina/Varian couple.
Most fans think Lars/Rhen is a better pairing than the canon Dameon/Rhen. Dameon successfully flirts with Rhen in the game, but there never seems to be a spark, even when they get gushy. Then it turns out that Dameon is The Mole (though already revealed to the players around the beginning of the game), making even less of a reason for that pairing. And then we have Lars, who was once cruel to Rhen since she was Made a Slave to his family, then finds out she's royalty, and he apologizes to her rather awkwardly. Though it is rather obvious the game tries to enforce the Dameon/Rhen pairing and tries to avoid Lars/Rhen, it is even more blaringly obvious that the Lars/Rhen pairing is far more popular in fandom. Build C of the game throws Lars/Rhen shippers a bone by adding an option to have Rhen go back to Shadwood Academy with Lars, only to state in the epilogue that Rhen did marry Lars... or did she?
Aveyond 3 gives us Edward/Mel. While it's possible to put them together in individual gameplay, the canon pairings are Edward/Stella and Mel/a descendent of Lars who doesn't appear in the game. It's not helped that in the trailer to the third chapter, it shows the Edward/Mel prologue, thus implying that Edward proposing to Mel was the canon ending of the second chapter.
Edward/Belf is pretty well-received for the lulz
Talia/Devin from Ahriman's Prophecy also seems rather popular. Like the Aveyond 3 example, you can put them together in individual game play, but the canon pairing is Devin/Alicia.
Morichika Rinnosuke has been paired with pretty much everyone despite not being in any of the official games (he IS in a few of the unofficial ones). The closest canon relationship is with Marisa, since she is more or less his little sister. Unsurprisingly, Marisa is one of the most popular ships. Oddly enough though, Keine is also one of the most common/popular ships (mainly due to the fact that they are both sort of half-demons, though Keine is really more of a werewolf), despite having no canon support.
Ace Attorney: Phoenix Wright is the man. Phoenix/Edgeworth is one of the most popular pairings (aided by the creators' tendency to bait their numerous fangirls), but Phoenix/Maya's pretty close. And Franziska/Adrian, forsomereason. You get a decent amount of Phoenix/Franziska too (but strangely, very little of Phoenix/Iris, the one canonical relationship the guy's ever had). And that's just scratching the surface here.
The one almost everyone seems to like, though, is Gumshoe/Maggey. Probably because it's pretty much canon, and pairing the two Butt Monkeys together is cute anyway. Almost everyone seems to like Diego/Mia, and Ema/Klavier from Apollo Justice, though Klavier/Apollo is quite popular too.
Edge/Rydia is extremely popular amongst fans, owing to their Belligerent Sexual Tension. Edge pretty much canonically having feelings for her helps as well.
People who hate Edge like to pair Rydia with Kain instead, based solely off of how Badass and popular the two are.
For those who sympathize with Kain, there's Kain/Rosa. Or you could go the OT3 route and have Cecil/Kain/Rosa, which is also pretty popular.
Bartz/Lenna from Final Fantasy V has a decent amount of fans despite the little evidence.
Bartz: "Yeah! You know, it was my dad's dying wish that I go out and travel the world... Plus, this time it feels like- like the wind is calling me."
Galuf: "What a sweet-talker! As if you don't just have the hots of the little missy."
Considering the fact that Bartz ends up traveling alone with two other girls, Bartz/Faris and Bartz/Krile also have their followers.
In Final Fantasy VI, a fairly significant portion of the fanbase ships Terra/Locke, despite the fact that Locke/Celes is the Official Couple. Celes/Edgar is also a fairly common ship, and the Japanese fanbase for Terra/Sabin is quite significant.
Setzer: Setzer reacts with interest when Terra's name is first mentioned, and Terra is the only person to ask Setzer a personal question during the whole World of Balance; when the world is destroyed,, it's Setzer who grabs Terra from the split deck of the Blackjack. Setzer will save Celes in the ending instead of Locke if Locke is not present. Celes will also encourage Setzer to fight Kefka and to recover his friends' airship, snapping him out of despair.
Special mention for the Kefka/Terra (Japanese) fanbase. There is definitely a good bit of fanart for them. Then again, Kefka was an evil megalomaniac with a very pretty young woman under his complete control; it wouldn't exactly be out of character for him to have a go. He certainly seems to be... excited by her killing skill.
Terra/Celes is incredibly popular, given that the two share only one brief conversation. They have a common backstory and party role, and they're the only conceivable femslash pairing, which lends them a great number of fics, particularly on AO3.
In Final Fantasy VIII, there's a pretty large Broken Base over the official couple of Squall and Rinoa. This has led to numerous factions that want to see him paired with other people...such as his rival Seifer, his teammates Zell, Irvine, and Selphie, and his former teacher Quistis. That's also leaving out the group that likes to see Laguna and Squall, canon be damned. Saying that any one is really preferred over another is a tough call, but there's enough fighting over the subject that it tends to lead right into Ship-to-Ship Combat... along with the fans that liked Rinoa and Squall. This dovetails nicely with the fans that just fight over whether or not Final Fantasy VIII is actually a good game or not.
By contrast another very popular romantic pairing via fandom is Fang and Lightning, which is labelled as "FLight." Aside from being inspired by the minor amount of Les Yay between the two in the game and the common understanding of Girl on Girl Is Hot. But on a more thoughtful level, the two are clearly set up as each others Foil (see the page) within the narrative, yet interestingly when Lightning is down it is Fang who props her up and in return when Fang is down it is Lightning who props her up. Finding hordes of pics, fanfics, and vids of "FLight" when simply just searching for just one of the two characters alone via Google, deviantART, YouTube, etc etc. is inevitable.
Serah and Noel from the sequel got a lot of supporters MONTHS before the game was even out, with some hoping that Snow and Serah had broken up because he wasn't seen in earlier trailers. And then it got even more support after the game was released and contained some very Heartwarming Moments between the two.
Let's not forget the humble, but growing number of Warrior of Light/Cosmos shippers out there.
It doesn't hurt that, WoL's strong and undying sense of duty to his goddess aside, it is eventually revealed that the pair are actually perfect manikins respectively modeled after Cid of the Lufaine and his wife.
Fans of Valkyria Chronicles vastly prefers the pairing of Selvaria Bles with Johann/Oswald the Iron. Considering what kind of dick Maximillian (the one Selvaria is canonically interested at) is, it should come as no surprise. Radi Jaeger is sometimes a decent substitute too.
Those who rather keep their ships in-universe like to pair Bayonetta up with Jeanne instead of Luke (the implied Love Interest), with whom she shares a good amount of Foe Yay (Jeanne being The Rival and all) andHo Yay, due to their rather... intimate... style of fighting. It's worth noting that Jeanne very much looks like a female version of Dante.
Alternatively, pairing up Dante with Morrigan from Darkstalkers. It's had a notable following for some time, which was only bolstered by their appearance in Marvel vs. Capcom 3. There is also a sizable number of people who have decided to save themselves the trouble and just turn the above two ships into an OT3.
Team Fortress 2: Any coupling outside of RED Spy/BLU Scout's mother and possibly Demoman/the opposing Medic's wife is based in Fanon, but the highly suggestive lines the Heavy has leads to Heavy/Medic being the most popular. Valve even shipteases these guys with the "Beaux and Arrows" achievement, which you get when you pin a Medic to a Heavy using an arrow, and the Medic-only Gentleman's Ushanka, which mentions the hat would match with the Heavy's ushanka.
BlazBlue: It's pretty known that Litchi is a Love Martyr for Arakune, but it doesn't stop people for pairing her with Bang. This gets even more prevalent when due to story development, Litchi's love for Arakune was one of the reasons why she pulled a Face-Heel Turn, thus if Arakune was not her main love, she would've no need for that. And surprise, Bang is revealed to possess a Nox Nyctores that might be the key to cure BOTH Litchi and Arakune and possibly annulling her Face-Heel Turn...
While Ragna/Rachel is getting more attention there is a following for Carl/Rachel mainly through their interactions in the first game (and to a much lesser extent the second).
Left 4 Dead 2 fans were drawing and shipping Zoey with Ellis way before their meeting and interaction in The Passing. Probably due to them being both the youngest and arguably most attractive looking in their groups. But still nothing compares with Nick/Ellis which has come to dominate the fandom with their Ho Yay. And ever since the release of "The Passing" DLC, Rochelle/Francis has also been a target due to how the two interact (they both hate stuff).
It's harder to make sense of shipping zombies, but there's a few Hunter/Witch shippers out there.
In the Resident Evil fan community, Chris/Jill has the most supporters since the firstResident Evil game's release. The second most preferred pairing is in fact Leon/Claire instead of Leon/Ada, although the latter has a sharp rise after Resident Evil 4. For the main antagonist Wesker, however, he has lots of Wesker/Redfield shippers somehow, with obviously some Yaoi Fangirls supporting the Wesker/Chris pairing.
As of 6, Piers/Chris has seemed to replace Wesker/Chris.
Prior to Mass Effect 2, the two main fan-preferred couples for Mass Effect were Male!Shepard/Tali and Female!Shepard/Garrus. The two were so popular, BioWare made them both official options, and they still take up the bulk of Mass Effect fanfic.
PokÚmon is a hard series to tackle, due to the numerous continuities and hundreds of shippings. Shippers tend to have a habit of shipping protagonists with each other, or rivals and protagonists, leading to those being the top shippings. Though Hilbert or Hilda/N is quite popular for their games, more so then the two protagonists together (as is Cheren/Bianca from the same games. Other possible combinations, like Hilda/Cheren and Hilbert/Bianca, do have followings but are fairly uncommon). Likewise, Cynthia/Dawn is almost as popular as said protagonist and either her rival or Lucas. Also, Silver/Lyra has a strong following.
Silver/Kris also had a fair number of shippers back when Crystal was released.
Interaction is not always required with common Pokemon shippings. For example, Morty/Falkner has a sizable following, even though Morty and Falkner are never seen interacting with each other. (They can battle each other at the Pokemon World Tournament, but the player does not get to see it.)
Despite Lux-Pain having a small fanbase, two of the main pairings that everyone can agree on are Shinji/Mika and Ryo/Hibiki. As for the main character himself, while he is shipped with everyone, the most popular pairing by default is Akira/Atsuki.
To put it simply, Akira/Atsuki has the mostShip Tease in comparison to the other potential love interests for Atsuki like Rui and Yayoi. Shinji/Mika is popular given that by pairing Mika up with Shinji, it greatly averts her being a victim of Die for Our Ship as well as evidence in the game that shows that she's moving away from Akira and getting close to Shinji. Finally, with Ryo/Hibiki, the fact that Hibiki is already confirmed to be in love with Ryo is one thing but whether or not Ryo has feelings for his best friend is up to debate although, there are some conversations that suggest that the feelings are mutual.
Spyro the Dragon fans tend to either be Spyro/Ember fans or Spyro/Cynder fans however Ember/Flame has managed to become rather popular despite the two never speaking to each other.
Harvest Moon fans typically cling to one or two pairings per game; for example Pony/Skye is probably the most common pairing for the Cute game. However for Harvest Moon: A Wonderful Life Nami/Mark is the most popular pairing in the game, for whatever reason.
The Mineral Town-based games have a straight example in Carter, the local priest; who is the most popular pairing for Claire.
While Frozen Essence lets Mina hook up with no less than five characters, the one who comes the closest to being a "default option" for her is Rune who she needs to pursue to get the True End. Naturally, the majority of players prefer Mina to be with Caius or Zareh instead; the former because All Girls Want Bad Boys, the latter because of him having been in love with Mina far, farlonger than anyone else.
Assassin's Creed I has Alta´r Ibn La'Ahad with Malik a-Sayf, which didn't stop even after the PSP game Bloodlines paired Alta´r with Maria Thorpe who'd been the unnamed female Templar in AC1. Assassin's Creed II and its sequel has Ezio Auditore da Firenze with Leonardo da Vinci, and confirmed the Alta´r/Maria pairing... not that that, or the fourth game pairing Ezio with Sofia Sartor has stopped the shippers.
Ditto for there being far more Shaun Hastings/Desmond Miles out there than the canon-suggested Desmond/the late Lucy Stillman.
There's also a fair number of loyal Ezio/Rosa fans, in spite of the official hookup with Sofia Sartor.
The most popular Assassin's Creed III ship is Connor/Aveline, despite (or perhaps because of) the fact that Connor has no love interests in his game and Aveline doesn't even appear in it unless you connect her PS Vita game to the PS3 version. Reams of fanart existed even before the games' release.
Despite Golden Sun fandom's notorious shipping wars for every other character in the series, Saturos and Menardi are near-universally seen as a Battle Couple, despite there being no canon evidence of romance between them.
Some pairings are still clear favorites even in the ship wars: Isaac/Jenna and Isaac/Mia dominate Isaac pairings, usually pairing Garet with the other girl. A lot of fans were irked when Isaac/Jenna became canon in Dark Dawn, not just because Isaac/Mia was sunk, but because Garet and Mia had children by unknown others instead of with each other.
Felix's most popular pairing is with Sheba due to his Always Save the Girl moment for her in the first game, which is given a nod in Dark Dawn's recap of the story. However, Felix/Karst is also wildly popular, since a lot of her scenes and dialogue can be read as Ship Tease, they were neighbors on good terms for three years, and there's that lovely hand-holding scene while she's dying.
In Skyrim, the Dragonborn and Serana from Dawnguard have been heavily shipped by the fandom, who praise her well developed character and how much depth was given to her burgeoning relationship with the Dragonborn. Many were disappointed that she's not a romance option, as despite the ship-tease, she politely turns down your proposal, stating her dislike of temples.
While Soul Nomad & the World Eaters has no Official Couple, Gig/Revya is the most popular. It helps that Disgaea games imply that their ending is canon if only because Revya travels with whoever has the highest affection for her at the end of the game and in Disgaea 3, Revya is traveling with Gig. Gig also doesn't stop talking about her in Disgaea 4 where he appears alone.
Every single couple has its fair share of fans in Avalon Code, but Anwar/Tia has a very notable fanbase, followed by Valdo/Tia and Ur/Tia. On the flip side, Yumil is often paired with Dorothea.
Contrary to popular belief, Luigi doesn't have an official love interestnote he sure as heck gets a lot of Ship Teasing, though, and there's endless Ship-to-Ship Combat between the two most popular Fan Preferred Couples for him, Luigi/Daisy and Luigi/Rosalina.
Inazuma Eleven has Endou and Aki apposed to the Official Couple Endou and Natsumi or Fuyuka depending on adaption though most of the fans got over it when they realized that she probably ended up with Ichinose.
In Mana Khemia: Alchemists of Al-Revis, the only ending with a confirmed romantic implication (not counting Vayne-as-queen in Muppy's ending) was with Nikki. And yet there's a lot of fan support for Vayne/Jess.
The Japanese Bahamut Lagoon fandom ships Byuu and Frederica despite there being little evidence, and Byuu and Yoyo, who broke up in-game.
For some reason, Hiroshi/Takuro is fairly popular in Ao Oni.
For Togainu no Chi fans, Shiki/Akira easily beats all other pairings in the English-speaking fandom. Granted, it is not more or less canon than any other pairing in the series. Meanwhile in Japan, Keisuke/Akira is very popular among the fans.
It's pretty much a common knowledge in the Wild ARMs 2 Japanese fandom that Lilika deserves Ashley much more than Marina does.
Goemon/Yae and Goemon/Sasuke are the most prevalent in Ganbare Goemon.
In Breath of Fire Ryu and Rinpoo/Katt in II is a popular Fan-Preferred Couple in both the US and Japan, even gaining its own Portmanteau Couple Name in English-speaking countries. Scias x Ursula in IV is a fairly well-established Fan Preferred Couple that has taken on a fanon life of its own. Ryu/Lin in Dragon Quarter is a similar case of a Fan-Preferred Couplenote considering the Nina in that game is all of twelve years old and Ryu has more of a Big Brother Instinct towards her..
Yaoi Fan-Preferred Couples abound as well. Probably the most popular examples include Fou-lu/Ryu which is technically a selfcest pairing in IV, Ryu/Bosch in Dragon Quarter, and Elyon/Jesuit in DQ.
Star Fox: In Japan, Fox/Falco dominates fan expression. There's a lot of it in the West too.
In Lamento - beyond the void there is a very sensitive war going on until today about who is Konoe's best choice for partner. Considering he have three options, it's not an easy discussion but Rai seems to be the favorite of the majority (and his ending is the so called "true ending" of the game).
Tomb Raider: Would you believe Lara/Doppleganger? At least it's the one that acquires most fanart. There's quite a bit of Lara/Kurtis and Lara/Amanda as well. Now with the 2013 reboot, Lara/Sam aka. S.S. Endurance, is VERY popular.
Eleven Eyes has Kakeru/Misuzu, Kakeru/Shiori and Takahisa/Yukiko.
In Dishonored a popular theory is Corvo is the lover of the Empress and possibly even the father of Emily.
Judging by the fanart for Morenatsu, the most popular Hiroyuki pairings are with Tatsuki, Kounosuke, and Juuichi. Ironic, since this art existed before the patch which completed Tatsuki's and Kounosuke's route was released.
Before DW6 of Dynasty Warriors, Sun Shang Xiang was usually paired with any of the "hot" Wu guys like Gan Ning, Lu Xun, Ling Tong, or Zhou Yu as opposed to her canon Love Interest Liu Bei. Koei seemed to counter this by making Liu Bei much younger and attractive looking in DW6. Before he looked a good 15-20 years older than her. After doing this there was a noted rise of Liu Bei/Sun Shang Xiang fanart and fanfics. Mission Accomplished.
Guan Ping and Xing Cai. Despite her being based on the historical wives of Liu Shan, Koei has teased that they might have feelings for each other.
On the yaoi side of fandom, Ma Chao & Zhao Yun have had a strong fan following for many years (arguably an example of a Token Minority Couple, given they were both young, handsome, almost exclusively pre-occupied with things like honor and justice, and up until DW6, spear-wielders) before Koei decided to make it official and actually give them an in-game friendship. With proper cutscenes! And special dialogue!!!! Whether it was Koei taking notes or just pairing up the spares is anyone's guess.
Fans of Eternal Sonata think that Chopin and Polka have better chemistry than the Official Couple... despite the fact A) she's analogous to his real-life dead little sister, and B) he's twenty-five years older. A lot of this depends on what version you're playing, though.
While there is no Official Couple in the game, the protagonist is capable of hitting on many of the girls, and thus many of them like him (which can really be said for everyone). However it's easy to see without the FATE route that Yamato develops as a person by just being in the protagonist's presence, originally seeing him as a pawn he can use, to seeing him as a capable leader, and then finally acknowledging the hero as his only friend that he can rely on. So if you take a route that isn't Yamato... he willnot take itwell at all. Given his backstory, though, it's understandable why he becomes clingy to the hero in the first place. The anime also doesn't help with upping Yamato's obsessive nature toward Hibiki and all the artwork promotes him, Hibiki, and Alcor (particularly one line where he tells Io that Hibiki is his, contrast to the game where he threatens to slash everyone's throat for daring to corrupt his hero).
The latter are popular more so in the anime than in the game. In the game, the two are partners but get separated because of Rolando attacking the Nagoya branch. Airi gets really angry if Jungo is killed and is relieved if he survives (mind you Jungo is one of the hardest people to save in the game). Jungo doesn't mind Airi using him as a way to vent her frustration and he always tries to cheer her up. Neither of them take it well in the game when they take different sides of the issue (she chooses law and Jungo goes neutral) when they fight each other in battle but are quick to forgive each other. In the anime Jungo is always saving Airi when she's in danger. Jungo puts Airi over everyone else in the party given his personality to save his friends. It makes their death painfully tragic because Jungo could have avoided his Death Clip but he chose to save Airi... but it ended up being in vain and Jungo realizes that when he stops running and holds her tightly before they're both blown up.
Pit and Viridi from Kid Icarus: Uprising could count as one, if the fan art and fanfiction have anything to say about it.
Dark Pit and Phosphora are often shipped together... for some reason.
Little Busters!: Rin/Riki is technically the official pairing of Little Busters, even if it's far, far more ambiguous than in most Key games, and certainly plenty of players ship it. But among the more serious fanbase, it's a lot easier to find Riki/Kyousuke or Rin/Komari fanart, and even Riki/Kurugaya is arguably as popular.
Ib: Almost all the fics on AO3 with a romance aspect ship Ib/Garry. There is no Official Couple for Ib, probably because the main character is nine years old and Garry, her preferred love interest, is anywhere from eighteen to twenty, but that hasn't stopped the fans.
While the Soul series is more preoccupied by violence and Rule of Cool than romance, subtextual or otherwise, fans nonetheless have a few:
Mitsurugi/Setsuka is popular as well, especially seeing as she defeats him in a duel sometime between the events of IV and V and consequently drops her grudge against him. Although this ship often clashes with the older, more established Mitsurugi/Taki ship, which has a similar allure.
That is to say nothing of the equally popular—and perhaps more popular where Yun is concerned—Yun-seong/Talim ship (spurred on by their interactions throughout II and III), which in turn has a surprisingly popular contender in the form of Talim/Link (not helped by the fact that in IV, Talim's joke weapons were a pair of ocarinas).
Kilik/Xianghua counts on a technicality. After four games' worth of Ship Tease and Unresolved Sexual Tension, from a Battle Couple moment at the end of the first Calibur all the way up to a (thankfully non-canon) bittersweetending in IV, there was no reason to believe that Kilik wasn't the father of Xianghua's daughter Leixia, especially when the girl was seen wearing his Dvapara-Yuga pendant. Naturally, many fans were none too pleased to learn that the two had parted ways between games and Xianghua went on to marry a Ming general named Yan Wujin and bear two children. Later on, it would be discerned that Kilik only left Xianghua in order to the protect the world she lived in, with strong implications that the two still love each other dearly. And guess who Xiba's parents are.