This doesn't mean that you have to like the canon, you can love any pairing you so wish. But just accept the fact that the pairings listed here are truth. And don't flame me over it; Skysplitter eats flames and all they serve to do is make me not like you for being such a childish ass.
With that disclaimer out of the way, we can start the show. Now, from how I see it, there are two main types of canon pairings...True and Hidden. True Canon Pairings are directly shown within the game or its sequels, by having the characters be affectionate to the point of romance with one another. Hidden Canon Pairings are officially endorsed and might show hints in the game and sequels, however it is not as in your face and might require a little more scrutinizing or analysis while playing, or having the supplementary materials such as Drama CDs, Artbooks or Manga/Anime adaptations.
True Canon 1 (Wedding Bells): This type of pairing denotes a couple who has been married at sometime within the game itself, the epilogue of the game or the sequel. The marriage can also have taken place between any two of these timelines...just as long as the game or sequel itself are living proof of the marriage. Some of these pairings are shown to produce kids, especially when the sequel stars their child, but some just show the wedding and leave it at that. There is also a small number of True Canon 1 Pairings that are married before the game, but generally they are not the main hero and his love interest.
In-Depth Example: Tales of Destiny: Namco's second Tales game is also the only game in the series to have a True Canon 1 Pairing for its lead hero (though there is at least one other previously married couple among the games). That's because ToD is the only one to have spawned a sequel, starring the son of the first game's heroes.
Stahn and Rutee were set up like your typical comedy anime pairing (I point you to Lina and Gourry of "The Slayers" who are so like ToD's heroes that it isn't even funny...right down to some of their quirks). They start off on the wrong foot and bicker over stupid things (such as Stahn being a Country Boy and Rutee being a little bit of a sneak thief). However, their fights generally are playful in nature, never to harm one another, and seem to be more of a running joke.
Eventually, Stahn realizes that Rutee is doing everything she does because she is trying to protect the people she cares about from starving (later on, those people are revealed to be the children of an orphanage where she was raised...and the mayor was going to demolish it for his wife to create an art museum unless Rutee got him the money). He saw her in a new light as a more sensitive person than she showed, and that Rutee had to hide behind a mask to keep from looking weak. Stahn decided to help her by giving her all his money and Lens before heading back home, as well as turning down the reward money for finding the Eye of Atamoni.
Throughout the second half of the game, Stahn was the emotional support that Rutee needed as she began to find out about her past and why she was in the orphanage. He helped her deal with the deaths of her father and brother, as well as extract vengeance upon Kronos for his role in their demises. She also provided some emotional support for him when he thought he couldn't go on after the death of Ilene, an older woman that he liked a little bit.
Though they were shown together in the ending picture as well as the opening FMV (as the only duo besides Garr and Chelsea which was shown as him protecting her like a big brother), it was still left up in the air what happened to them or if someone else stole Stahn's heart away. Finally, several years later, ToD2 was announced for the PS2. And when its lead character was first introduced, the boy was said to be Stahn's son, Kyle. Not to long after, Rutee was revealed to be his mother.
From the years between the two games and the child's age, we were finally able to get a small picture of how things came together. Stahn would have had to marry Rutee about a year after the reunion at the most since Kyle was born three years after the war. Sometime between the reunion and the marriage, he moved in with her and helped raise the orphaned children in Cresta. And once the timeline was fixed following Kyle's adventure, Stahn and Rutee were able to lead a happy life together with their son and the other children.
Other Games With This Canon...
Lufia II: Rise of the Sinistraels
Marl Kingdom Trilogy
True Canon 2 (Dating Fools): This type of pairing denotes a couple who are shown to be deeply in love but their marriage is never shown in the game. It may be revealed in a Drama CD epilogue, sequel Manga or Artbook...but not all fans have access to those (especially outside of Japan). Unless the sequel involves either a far off timeline in the same world or the same characters within five years of the original, generally the game in question is a stand-alone (as a sequel of more than five to ten years will generally have to show some kids and thus elevate it to True Canon 1).
In-Depth Example: Tales of Destiny 2: Partly because they are younger and more innocent than Stahn and Rutee were, and partly because of the lack of a third ToD game, Kyle and Reala of Tales of Destiny 2 represent the step below what his parents were. However, their love is still shown to be true throughout the game.
Like Stahn, Kyle devotes himself to protect Reala so that he might prove himself a true hero. He guards her more physically than his father had to do for his mother, though there is still some emotional support needed in a few instances. Though at first she wanted to do everything on her own, she eventually accepted Kyle's offer to help her find a hero, and was extremely happy when he eventually proved himself to be the one.
Several times the two went on dates together. Twice it was to the park in Heidelberg (of course, both of those times were interrupted by the enemy...but the thought was there) and they also went together to the Laguna Ruins to talk before the final battle. These dates were used as character building exercises as well as to show how each supported the other when they were down and out.
Reala trusted Kyle enough to give up her life, knowing that it took people like him to better the world and not Fortuna controlling every aspect of human life. She was the one insisting he destroy the Lens, knowing it would end her life, because she felt that Kyle's freedom was worth more than her existence. Kyle, meanwhile, struggled with having to fulfill his duty because he couldn't bear to hurt the girl he loved.
But Kyle's goodness was rewarded. When he returned to the Laguna Ruins in the rewritten timeline, after Loni had left the room, he heard a voice call out his name and Reala appear before him. Even though his memories regarding the adventure were gone, his heart remembered her name and he called back to her before she jumped into his arms. Because their love was so strong, Reala was able to come back to life when she otherwise should have remained dead. And like Stahn had told him before he left, Kyle had found "something irreplaceable" while on his journey...someone to love.
Other Games With This Canon...
Lunar Series
Most Final Fantasies
Hidden Canon 1 (He's a Ladies Man): This type of pairing denotes the canon hidden among an RPG where hooking up your character with another is a fun little side event. In some shape or form, through special events and in-game choices, you are given the options of changing how your main character (and sometimes even the allies) feel about the others in the party. If you do things right, you will be able to produce an ending between those two characters that plays after the main story wraps up. These endings can range from being friends, dating or even married and expecting a child.
However, even in these cases there generally is a canon. It may be confirmed in other media (Drama CDs, sequel manga, sequel games, Artbooks). The canon lover is also, for the most part, the easiest person to hook up with the main hero, requiring the least amount of manipulation and can sometimes be done without knowing what the hell you are supposed to do to change things.
In Depth Example: Tales of Symphonia: Taking a leaf out of the books of its cousins in the Star Ocean series, ToS tried its hand at giving you an option as to who to hook up with who. Though only Lloyd could have his fate chosen and the scenes at Flanoir and Heimdall as well as the kidnapping of your Soul Mate were affected more than the ending, it still gave you some control over who his interest was. However, that didn't change that Namco had officially hooked him up with Colette.
Lloyd was protecting her from the start of the journey. He felt concern as her humanity was slowly being stripped away by the transformation into an Angel. When she lost her voice, Colette communicated by writing her words on Lloyd's hand with a finger. It was also a threat against the present that he'd made her which brought her back to herself after losing her humanity, when the Key Crest itself didn't work.
A big thing that illustrated the choice was the incident when Lloyd's Soul Mate is kidnapped and the team heads to Derris-Kharlan to save him/her. The characters are split up in groups of two after trying to go past a teleporter, and Lloyd must find where they are. Each person is in a set grouping (The Fugitive, The Judged, The Neglected), however Colette will take the place of whomever your Soul Mate is if anyone except her or Kratos was chosen (if Kratos is chosen as the Soul Mate, the Heimdall scene between Lloyd and the chosen person is skipped and Colette follows all the usual Soul Mate duties from the kidnapping onward, another point in Colette's favor as the canon pairing).
Though Colette can easily be fit into those categories, and the scenes flow smoothly, there are some things that are odd about them...
If Zelos is your Soul Mate, Sheena still says "Looks like he beat me to it" when Colette goes down to join Lloyd after they break free of Mithos' illusions (seeing as either Kratos or Zelos were there normally, they didn't bother to program in another line for her).
If either Raine or Genis are your Soul Mate, Colette is then thrust into either arguing with the mayor (Genis) or Remiel (Raine) over her role as the Chosen. When Raine and Genis are there together, they argue with the mayor (Genis) and their mother (Raine) over the issues involving them being Half-Elves. The issue changes a little when half of the discrimination piece is removed (since that is a main theme of the game).
If either Regal or Presea are your Soul Mate, Colette changes her role based on who remains in the scene. When Presea is your Soul Mate, she will defend the illusion of Alicia, though she really has no reason to think it's real. When Regal is your Soul Mate, she sees through it and fights with Presea to wake her up.
The only person she can replace without any oddities or inconsistencies is Sheena, because Zelos doesn't say anything too character based towards the ninja girl. However, other evidence in the game still shows Lloyd is meant for Colette. Also, he is shown with her twice in the opening FMV: her writing something on his hand when she couldn't speak, as well as the two of them together in Flanoir (probably to indicate that talking to her was canon). If you don't do too much manipulation, she will most likely be your first choice at Flanoir (it might be easier to dislodge Genis and Sheena, who I generally seem to get as the second and third without much manipulation, since you can say no to up to the first two and still keep Zelos in your party by going with the third).
Other Games With This Canon...
Star Ocean Series
Most Fire Emblems
Fun Fact: Both Claude of Star Ocean 2 and Roy of Fire Emblem: The Sword of Seals are the children of other characters in the series (Star Ocean 1 and Fire Emblem: The Blazing Sword). Due to the nature of the games, though the identities of their fathers are known, their mothers' names are never revealed within the games itself (Claude's mother is offscreen in his solo ending and Roy's mother is dead). However, the pairings are subject to the rules of this canon and thus are hidden within their fathers' games themselves; though the remake of Star Ocean 1 seems to practically confirm the identity of Claude's mother by making her have several key similarities to him, and also make her and Claude's father have one of the few altered ending scenes and the only ones for those two.
Hidden Canon 2 (We Won't Tell): This type of pairing denotes the canon not being officially confirmed within the game or sequel itself, but hinted at greatly. There might also be confirmation on anything up until and including weddings and children within supplementary materials such as Manga sequels or Artbooks, however if you just play through from start to finish you wouldn't find it. Sometimes, there might be another girl or two around for the hero to be attracted to or vice versa. However, officially the issue has been sorted out by the company if only in a blurb in an interview. This type of pairing is also the most debatable about whether or not it is canon.
In-Depth Example: Tales of Eternia: For those of you who don't already know, ToE was released in America as Tales of Destiny II (we get questions as to whether or not ToE and the real ToD2 are the same game all the time so I had to point that out). Something about Matel and He-Man owning the rights to the word Eternia...and instead of shortening it to Eternity they decided to leech off the (relatively small cuz it's not Final Fantasy and doesn't have a high graphics engine) popularity of Destiny by borrowing the name.
Let's not mince words...Reid gets with Farah and Keele gets with Meredy. But considering the first three were all friends in childhood, Farah and Keele have been paired together at times. And Meredy also senses Reid's hidden powers and finds herself stuck on him early in the game, leading to that pairing having fans. To the best of my knowledge, other than Reid and Farah staying on Inferia and Keele going to Celestia with Meredy there is no real closure on the pairings. No kissing, no hugging, no marriage, no children.
But throughout the game, the majority of interraction for Reid is with Farah. He's jealous of her friendship with Ras because he fears she'll like him better. They're supportive of each other in times of roughness. And it's Keele and not Reid who gives Meredy the boost she needs at the end of the game.
If you can't tell, I haven't played ToE in awhile. But I do know the canon and would appreciate feedback to help me flesh this out a little bit.
Other Games With This Canon...
Too many to count; there are many of these that are debatable as to whether or not there is a canon pairing for the hero.
Proof Of The Tales Canon As Shown By Namco
Tales of Fandom Gaiden Subbed Part 1
And Part 2 (they all say their girlfriends' names here)