There's a fairly big fanclub for Danny/Juniper Lee (The Life and Times of Juniper Lee), though some find it squicky because of the age difference. Though once June is aged up from 11 to 13, there is less Squick.
Danny has been paired with both Raven and Starfire from Teen Titans (2003).
There are some Youtube videos that pair Danny with Bloom from Winx Club.
Danny's older sister Jazz tends to get paired with Jason Todd, in large part due to crossover fics with Batman (and the DC Comics universe at large) being quite popular.
Tumblr once exploded with Norman (ParaNorman) and Dipper (Gravity Falls) fanart tagged under Parapines. This mostly seems to stem from their supernatural connections and general adorableness. Examples: [1][2][3]. The Norman and Dipper shipping grew into a sort Multi-player crossover entitled Mystery Kids or Spook Crew. Members include but are not limited to Dib (Invader Zim), Raz (Psychonauts), Coraline, and Courage the Cowardly Dog. Examples: [4][5][6][7][8][9].
Popular "Mystery Kids" character roleplay blogs have Fanonized Dipper/Norman and Coraline/Mabel. See here: [10][11][12][13].
There's also the shipping Pinescone, which ships Dipper with Wirt (Over the Garden Wall). They're both dorks and both have funny siblings. So, why not?
There's also Grunkle Stan/Eda Clawthorne (The Owl House), due to their similarpersonalities. Adding some fuel to the fire, the episode commentary for "The Land Before Swine" provides a description of Stan's ex-wife "Marilyn", claiming she has pale skin and a weirdly sharp tooth, and that "Marilyn" wasn't her real name. This leads many to believe that "Marilyn" is an alias for Eda, which was confirmed in The Owl House episode "Yesterday's Lie", which has an autographed picture of Eda using "Marylin" as an alias while in the human realm, giving the ship even more steam.
Yellow Diamond or Peridot have been shipped with Bill Cipher from Gravity Falls. There's a consistent joke in the Gravity Falls fandom that Bill resembles a Dorito, and the same joke has been applied to both Yellow Diamond and Peridot for their triangular designs and yellowish color.
At least two crossover fanfics ship Connie with Lincoln Loud (The Loud House).
White Diamond and Tamatoa (Moana) is rare but not unheard of, most likely fueled by the latter's obsession with shiny objects and popular FanonAlternate Universe Fics giving Tamatoa powers not unlike those of White Diamond.
There's one fanartist who draws fanart pairing Lincoln Loud with Katie (Phineas and Ferb).
Lisa Simpson from The Simpsons is the Launcher of a Thousand Ships in some crossover fics. She's been paired up with, to name a few, Dalek Sec, Starscream, Waspinator, Jack Harkness and Randall Boggs of all characters, although, with the exception of Captain Jack, those were all subtext.
Avatar: The Last Airbender Azula gets paired with WALL•E. Because there is no better way to help cure Azula of her Villainous Breakdown. (This is a friendship pairing, not a romantic one, mostly because if EVE found out, Azula would not survive the night.)
Blossom from The Powerpuff Girls and Aku from Samurai Jack even has a fan-following on deviantART. One artist, teacupballerina, draws a lot of pictures about this ship.
Jack isn't left out however as he's shipped with Johnny Bravo to make "Samurai Bravo". It all started from the Laundry Day bumper with Johnny in a goofy bathrobe and Jack in his Fundoshi.
Pairing him with Twilight Sparkle is even more popular, with tons of fanart as both humans and ponies. Not all of it safe for work.
And, as of 2013, the surprisingly congruous pairing between the aforementioned Pegasus and the frog that friends forgot (Sgt. Frog) has been birthed into the world through a miss DevilCove of DeviantArt.
Among bronies and Trans-Fans who are also fans of both Transformers and Friendship Is Magic, Princess Celestia/Optimus Prime is surprisingly popular. Likely given considering similar personalities and roles.
Lots of pairings combining Man Six with Team Fortress 2: Applejack with Engineer, Rarity with Heavy and Spy, Pinkie Pie with Soldier, Pyro, Heavy and Scout, Fluttershy with Medic and Heavy, Rainbow Dash with Scout and Soldier, and Twilight Sparkle with Sniper via Youtube.
Chances are one might see Pinkie Pie paired with Loki.
Loki's also been paired with Twilight Sparkle and (jokingly) Big Mac.
Applejack has been paired with Grumpy Bear and Rainbow Dash with Funshine Bear in the surprisingly rare Care Bear/Pony crossover fan fictions.
Semi-related, unpopular example: Pinkamena Diane Pie from the infamous Cupcakes (Sergeant Sprinkles) and Audrey II from Little Shop of Horrors have been paired together. Yes, there's a pairing between a murderous, fun-loving pony who enjoys torturing her subjects and a manipulative, singing, man-eating plant that needs blood to live. This unholy union may doom everypony, but they'd make a killer duet.
A common meme: Derpy Hooves/Doctor Hooves (Doctor Who). Semi-arguable; there's a pony in the show who (somewhat) resembles David Tennant, so whether this is a full crossover or not is the debate point; some fics treat him as the Doctor if he had always lived in their 'verse, others have him arriving and dealing with life in Equestria. Ascended Fanon as of the 100th episode. The episode implies Doctor Whooves is the Doctor and he is friends with Derpy Hooves.
Rainbow Dash X (Classic) Spyro the Dragon is not unheard of, thanks to them having similar personality types.
There's also Spike X Ember (from the same series above). Whether Spike gets a Plot-Relevant Age-Up or not seems to be optional with most people.
Another Hatchling, crossing My Little Pony: Friendship Is Magic with Metroid, ends with Twilight Sparkle and Samus Aran in bed together. Their adoptive son Spike's reaction, when he finds them, is "Well, that escalated quickly..."
KnightMysterio's Friendship is G.I., a crossover between MLP and G.I. Joe: A Real American Hero, has Beachhead and Tempest Shadow falling for one another due to their shared personality types.
Azula left Doom, complete with a "Dear John" letter. Apparently the good Doctor has rebounded and is going out with Squirrel Girl, but rumors of Azula returning are flying around.
Prinack- a couple consisting of Jack Spicer (Xiaolin Showdown) and Teen Princess Morbucks (The Powerpuff Girls) was made popular by DeviantArt artist,Callyie-Chan She draws most of the fanart and has a medium following by the Powerpuff Girls fandom, and somewhat of the Xiaolin Showdown fandom as well. There is a fan club also. This couple could also count as a Theme Pairing due to the following tropes.
Harmless Villain: There was a episode where Blossom regarded Princess as such and we all know about Jack.
Parental Neglect: Jack's parents are never there and we never see Princess' mom. It might be implied that her parents got divorced or she works overseas a lot. Also, King Morbucks doesn't seem to have an interest in her well-being and he's only around to give her money when she asks for it.
Lonely Rich Kid: To an extent. Neither has siblings and nobody really likes them much. It's also impiled that Jack comes from a wealthy family like Princess. That would explain his fancy house and he ability to build almost an unlimited amount of robots.
Owen Dennis, one of the storyboard artist on Regular Show, is shipping Mordecai, from said show, with Godzilla. And he's posting images of the couple on Tumblr.
There's a surprising amount of fan art and fanfiction on the net featuring Fifi from Tiny Toon Adventures with Tails from Sonic the Hedgehog. Granted, they're both the Ensemble Darkhorses of their respective series, and Tails is a Launcher of a Thousand Ships, but one could argue it's more common than Fifi X Hamton, the shows canon pairing.
Carmen and Shego from Kim Possible has been thrown around due to the similarities in their characters (dark haired ex-good guys who are chased by redheaded teenage heroes and their blond male friend). On the other side, some like to joke that they're mother and daughter due to the comparisons and say Shego's last name (Go) is short for "Sandiego".
Something between Wally from Where's Wally? and Carmen is a common joke. Carmen is the world's best thief who always gets away so who better for her than the man who is incredibly good at hiding? Where are they? At least their small-but-growing fandom is easy to find, not so their child.
Thanks to a certain fan-artist the idea of Carmen and Valerie Frizzle from The Magic School Bus is a thing.
Many anime fans pair her with Lupin III due to how much they have in common. They're both world class thieves who steal not just for gain but also for the fun and challenge of it, they both treat it as a game and they both like to leave clues for the detectives who are determined to track them down.
There exists an ongoing crossover fic pairing Azula from Avatar: The Last Airbender and Soren from The Dragon Prince, and the author has a tumblr blog dedicated to the pairing. Both shows share much of the same crew and talent, such as Aaron Ehasz, so while these two characters being shipped is suprising, the two shows being crossed over is not. Initially done as a crackship, and still often played for humor, the author plays the romance fairly straight and offers in-depth character analysis on why it works.
Marinette (Miraculous Ladybug)/Damian (Batman), called MariBat or Daminette, is becoming a popular ship among the Miraculous fandom. It started out as an AU created by ozmav and then it exploded. This Crossover Ship AU is popular enough that it has its own page. There is also an Tumblr archive for fics and fanart of this ship.
Shipping Korra with Naruto is quite popular due to the fandom overlap between the two series. Korra fans who dislike shipping her with Mako and Bolin, and Naruto fans who dislike the Love Triangle from early in the series, ship the two in response.
Stan Pines x Eda is gaining popularity due to their similarpersonalities. It's fueled by the Easter Eggs hinting that Eda is the Marilyn with whom Stan was married for six hours before they divorced.
Eda would probably be good friends with Alice, since they're both old yet feisty.
Amity would probably befriend Catra due to their similarissues and complicated relationships with Adora and Luz, not to mention that the former has a cat palisman and the latter is a Cat Girl. Glimmer and Eda would probably bond due to their respective recklessness and they would likely form a bond similar to what Eda has with Luz. Lilith and Angella would bond over having to deal with relatives like them.
Luz and Akko would get along swimmingly as they both desire to become powerful witches while Amity and Diana would get along with the similarities of their heritage of being from powerful families (but actually being nicer after meeting up with Luz/Akko).
It's been suggested on social media that Hooty and Duo would make a great couple. Even Dana Terrace and the Duolingo Twitter commented on it, though the former (possibly jokingly) discouraged it, on the grounds that they were "bitter rivals" in the bird industry, but have come to respect each other after teaming up to fight the owls of GaHoole.
Anne and Luz are shown to get along quite well for having many similarities.
Some think Luz would bond quickly with Marcy, due to being young girls with Ambiguous Disorders that see being trapped in another world as a dream come true. Marcy would love to go to Hexside, given how excited she was to learn about witchcraft from Maddie.
Hunter and Marcy already have some fan-art, a fan-vid and even a fanchild. No one knows how it got so popular, but Hunter already being a Launcher of a Thousand Ships may be the cause.
Many have joked about the idea of King Andrias and Emperor Belos either teaming up upon realizing how similar they and their goals (or at least Belos' smokescreen for his real plans) are or becoming a couple.
A portion of fans from Latin America ship Amity with the animated El Chavo, although not seriously and only as a meme.
Lightning The Pikachu originally had Guapo Flub and Alfe as close friends due to both being hated characters who love food and cause problems but save the day afterwards, and both being jerks to their best friends/brother figures. However, she started shipping her new duo as a joke until she got comfortable with the idea of making them a couple in her stories and fanart.
Danny and Kim from Kim Possible.
