Before the series came out, Ruby and Weiss were shipped together constantly. This was most likely caused by the DeviantArt author LunarisFuryAileron, whose RWBY4komas were featured on Monty's Twitter a few times. This continued on even after Ruby and Weiss were revealed to have very different characterizations than what the fandom assumed.
Blake and Yang shared almost no interaction before they became teammates halfway through Volume 1, but that hasn't stopped the so-called Bumblebee pairing from being one of the largest pairings in the show. Fans were delighted when the show teased them together in a little heart-to-heart talk in Volume 2.
Unfortunately, near the end of Volume 1, the above led to newcomer Sun Wukong being the subject of much hate early on,when he appeared to be getting close to Blake. Theories sprang up fast, ranging from him being a secret member of the White Fang to a killer out for Blake's head. To the surprise of very few, this hate evaporated when his other male teammates were revealed, where he was promptly shipped with his newly revealed Casanova Wannabe teammate Neptune... Based on Neptune's design alone. Despite Sun's focused continued interest in Blake, and Neptune's later interest in Weiss, both interests are commonly ignored in fandom to ship both together. Pair the Spares in a world where Everyone Is Gay.
Enough comments appeared on the Worm threads shipping Skitter and Clockblocker together that the author had Clockblocker explicitly sink it in canon.
Beyond Skitter/Clockblocker, other pairings like Skitter/Panacea and Skitter/Tattletale tend to be much more popular than canon pairing Skitter/Grue.
It would probably be easier to name the This Is It fanfics and fanart that don't ship the Notebook and Tony the Talking Clock. The two of them have never interacted, and they've never been onscreen at the same time for more than a few seconds.
Nyan~ Neko Sugar Girls fans overwhelmingly ship Koneko and Raku despite the fact Raku pines for Hitoshi the entire series. The finale where Raku dies in Koneko's arms as she cries only cemented the pairing. Prior to that Kidnapper-kun/Hitoshi was the most popular ship until it became the Official Couple.