JonesyGarcia and NikkiWong of 6teen have known each other since they were in Kindergarten—they got together sometime between the end of Season 1 and the beginning of Season 2, but break up three months after they first started dating (at Nikki's insistence). However, they get back together in the last episode of Season 2, after Nikki confesses that the real reason she broke up with him before was because she was afraid that if their relationship ultimately didn't work out, they wouldn't be able to be friends again and she'd end up losing the one guy she ever genuinely cared about—they remain together for the rest of the series. And in the series finale, when Nikki and her family end up moving away, Nikki and Jonesy decide to commit to a Long-Distance Relationship.
Ginger Foutley and Darren Patterson from As Told by Ginger. In the end of the show's run, we see that after their breakup they eventually get back together at some point. And are shown to be married and have a baby girl with ginger hair, in the distant finale.
Atomic Betty: Noah has a long-standing crush on his best friend, the titular character. Naturally, she doesn't notice his feelings for most of the series. She does become aware in the post-episode short "Bizarre Love Triangle" when Sparky, DeGill, and X-5 spy on Noah with his webcam, revealing his feelings to Betty when she walks in on the trio. So far, she hasn't done anything about said knowledge.
Avatar: The Last Airbender: Mai and Zuko had a crush on each other when they were kids; there's a flashback to show it and Azula confirms it in the in-between comic "Going Home." Mai's still interested in him during the main narrative and he, ultimately, reciprocates.
Ikem and Ursa in Avatar: The Last Airbender The Search. Ikem confessed he loved Ursa since they were six. Ursa happily agreed to his marriage proposal, but soon met Ozai and went into an Arranged Marriage with him, due to a prophecy involving their bloodlines. The fact that Ursa still loved Ikem is a major factor in the Dysfunctional Family she and Ozai had with their children.
Babar and Celeste's relationship in the animated series and film, eventually moving into Happily Married as adults. Notable in that, in the books, they were cousins, whereas the series ignores/changes that particular aspect and makes them unrelated to one another.
Lazlo and Patsy in Camp Lazlo. In the episode "Spacemates" it is revealed that Patsy and Lazlo are soulmates; and that they will be together in the future forever.
From Chowder, the aforementioned protagonist and Panini as revealed in the finale.
In Code Lyoko, Sissi Delmas reveals in episode "Marabounta" that she's in love with Ulrich Stern since kindergarten. Her lack of success wooing him doesn't come so much from him seeing her as a friend, though, but more from Ulrich simply not liking her.
Word of God states that Manny and Frida of El Tigre become this sometime after high school. This is to be expected as the show was created by a husband-and-wife team who made the show from experiences they had when they were younger.
Timmy's parents themselves are this. Though Timmy's mom had been with Dinkleburg until their college years, when he dumped her.
The Flintstones: Pebbles and Bamm-Bamm have known each other from infancy — and their relationship, ultimately, ends up in marriage.
Jerrica from Jem met Rio at age ten when he moved next door and instantly fell in love. It wasn't until high school that they began dating. Since then they've been more-or-less going steady, though the fact Rio is in love with Jerrica's new Secret Identity is hurting things. There's even a song about them called "First Love".
Kim Possible and Ron Stoppable (they provide the main page image). The biggest roadblock to Kim's and Ron's Relationship Upgrade, mostly for Ron (it's one of the reasons he decided not to risk it during Kim Possible Movie: So the Drama) was their long friendship. The roadblock for Kim not dating Ron was because of falling to peer pressure, as well as doubt about Ron's level of maturity, but the trope still stands. As Kim points out when Bonnie forces herself on Ron, it took them twelve years to actually kiss.
In The Legend of Korra Tenzin and Lin Beifong, who have known each other since they were kids, were a couple in their younger years. However, they broke up after they began to have "different goals" and Pema confessed her love to Tenzin.
Candace and Jeremy who met in late elementary school.
It's been stated (in-universe, not Word of God. Time-travel was involved) that Isabella is going to marry either Phineas or Ferb. Isabella and Phineas end up dating in college.
The Raccoons: Married couple Ralph and Melissa Raccoon have known each other since they were kids.
The Ridonculous Race: Racing partners Carrie and Devin said that they knew each other since they were kids, stating they first met at a sandbox when they were five. Their relationship turns romantic over the course of the race.
In Rugrats, since Kimi's introduction in Rugrats in Paris, she and Tommy were often paired together during their adventures and both had similar traits and personalities (during their infancy). This possible pairing was assumed, due to Kimi being Tommy's female counterpart. However, things do not look so good in All Grown Up!. But despite their interests in other one-time characters (Z; Olivia, Rachel, Anita), Tommy already dating his girlfriend, Rachel (up until their breakup), and their disinterest in each other (possibly out of respect for Tommy and Chuckie's friendship) in the episode "TP + KF" where the pairing is finally touched on, it is hinted at the end of the episode that they have a slight interest.
The Rupert episode "Rupert and the Mulp Gulper" had a scene that implied that Rupert's parents were in love since they were children. Mr. Bear reminisces on how he used to test his abilities at the carnival games to impress his girlfriend. Mrs. Bear then adds that she certainly was impressed and proceeds to affectionately cuddle with her husband, making it clear she was the girlfriend Mr. Bear was referring to.
She-Ra and the Princesses of Power: Catra and Adora have been best friends since they were children, which makes their animosity throughout the series all the more painful. Despite their animosity, it's clear they care for each other, and their relationship always has certainundertones. However, in the final season, Catra makes a HeelFace Turn and they repair their friendship, before finally admitting in the series finale that they're in love, sharing a kiss to seal the deal. The Beta Couple Bow and Glimmer are also this trope: they too have been best friends all their lives, but it isn't until the series finale that they admit they love each other romantically, sharing a forehead kiss before the final battle.
Homer and Marge met when they were children. They are an interesting case, in that neither realized that they had met as children until long after they were married. Both thought that they had met in their senior year of high school.
Sonic the Hedgehog (SatAM): Sonic the Hedgehog and Sally Acorn are revealed to have known each other since the age of five in "Blast to the Past Pt. 1 & 2", and the two grew a strong relationship before finally revealing their feelings for each other in the (unintentionally) last episode of the series. Their relationship would eventually carry on in the comic adaption.
Peter and Gwen Stacy in The Spectacular Spider Man. By the end of the series she had actually gotten him to reciprocate, but they were dating other people at the time; she was unable to immediately break up with her boyfriend, Harry, because of the "death" of his dad, and before that could get straightened out the show was Screwed by the Lawyers. If the show had continued, Peter would probably have ended up with Mary Jane anyway.
Star vs. the Forces of Evil: Marco has been crushing on Jackie since kindergarten, but he gets so nervous around her that he hasn't made any progress with her in all those years. He finally asks her out in "Naysaya" and they start dating in "Bon Bon The Birthday Clown".
She breaks up with him as she realizes he's better off with Star, and he and Star hook up by the end of the fourth season.
In Teacher's Pet Leonard and Leslie who have been best friends since they were babies. Leonard fell in love with her first and Leslie started to fall for him in season 2. In the movie, they kiss on the lips and they finally end up together.
Aqualad had a longtime crush on his friend Tula, even considering leaving the team to be with her. Unfortunately for him, she began a relationship with his best friend Garth during the time he was away. He understood and wished them the best.
Barbara Gordon is described as "Dick Grayson's oldest friend," and her single line of dialogue in season one was getting annoyed when he paid attention to another girl. The tie-in comic delves into this a little further, showing that she did confess to him on his fourteenth birthday, which immediately cuts to them kissing on his nineteenth birthday. We know that Dick's had several relationships during that five year gap (one starting exactly 31 days after that confession) and they're not explicitly a couple, because Dick, at nineteen, isn't ready to settle down and Barbara knows it, but there is an understanding that they love each other.