Note: This is a short and very incomplete list in constant need of updating.
Canon Romantic Relationships (see discussion)
As of season 4, the only confirmed on-screen romantic relationships on the show are:
Scott McCall and Allison Argent.
Scott McCall and Kira Yukimura.
Scott McCall and Malia.
Allison Argent and Isaac.
Lydia Martin and Jackson Whittemore.
Lydia Martin and Aiden.
Danny Mahealani and Ethan.
Stiles Stilinski and Malia.
Derek Hale and Paige.
Derek Hale and Kate Argent.
Derek Hale and Jennifer Blake.
Derek Hale and Braeden.
All other potential pairings still fall under the realm of fanon. However, the canon status of a pairing - or lack there of - has no impact on the ability of fans to ship whichever characters they choose. Ship and let ship!
Pack Meetings, Pack Night, Pack-Bonding Exercises, Puppy-piles, and everybody-lives-at-Derek's-place are all fanon tropes so far not seen anywhere in an actual episode.
Fanon has it that the Camaro was Laura's but the show hasn't addressed this assumption.
Canon has not shown Derek to be Scott's beta or a part of Scott's pack at all after giving up his alpha status to save Cora. Instead, he is often shown working independently or with the other adults on the show. This is especially evident given that Derek leaves Beaconhills for extended periods of time at the end of both seasons 3A and 4.
Stiles' first name as of season 4 is still unknown. Fandom popularized Genim or Gemin. (However, Jeff Davis has confirmed that neither is his name.
Stiles Stilinski has a bedroom window but we've never seen anyone in an episode crawl through it.
Roscoe the Jeep
Stiles' Jeep. Dubbed Roscoe in fandom thanks to a headcanon shared by Dylan Obrien.
The fandom notion that Stiles carries a bat predates Stiles stealing the bat from the McCalls in canon.
The Sheriff's name is John, according to fandom.
The Sheriff isn't shown in an episode to have any health problems, despite Stiles' worrying.
The fanon surrounding Malia is the source of a lot of hate toward Malia's character and wank in fandom in general. Malia was in her coyote form for 8 years. Fans, rightly, assumed that this meant that she would be developmentally stunted--a mental 9-year-old once she turned human again.
However, Canon has clearly shown that this is not the case. She is presented as a fully functioning teenager, with an advanced vocabulary and mature understanding of the world. Whether or not this is sensible or realistic, it is canon. Objections to her character or her character's capabilities that base themselves on the "mental age" she "should" be are based on entirely on fanon and on assumptions built up within fandom after her initial introduction but before anything more about her was elaborated upon.