Empowered has a Shipper on Deck in the Caged Demonwolf who's convinced that Empowered/Thugboy/Ninjette are hot for each other. It doesn't help that while Emp and Thugboy are an Official Couple there's a lot of UST between Thug and Jette. Adding to the possibility is that Emp herself is a "three-drinks-bisexual" and Ninjette has experience in girl-on-girl as part of her ninja disguise skills.
Sonic the Comic: Both Sonic/Amy/Tekno and Amy/Tekno/Shorty get thrown around by those who think Tekno and Amy would be a good couple, but also like them with the boys they're given Ship Tease with.
The comics had already had the Canon Foreigner Sally Acorn as Sonic's love interest when Amy was introduced. The over 5 year age gap between Amy and Sonic meant that that Amy's crush wasn't initially an issue, but then Amy got a Plot-Relevant Age-Up and the Ship-to-Ship Combat really began. To resolve this, Sally/Sonic/Amy is one of the most popular OT3s in the franchise.
Knuckles had a Canon Foreigner girlfriend, Julie Su, when Rouge was introduced. Rouge and Knuckles have a lot of Ship Tease in the games. As a result, people began pairing up Julie Su, Knuckles, and Rouge.
Shadow, Rouge and Amy also has a decent following based on many arcs about Shadow, maybe due to Amy and Rouge playing as Shadows guides to help him do what's right
In Spirou & Fantasio, the Ho Yay between the titular characters is rounded out by Seccotine's semi-canon relationship with Spirou and her chemistry with her enemy Fantasio.
Strangers in Paradise has the wildly popular fan pairing Katchoo-Francine-David, though canon is a lot more complicated; see Polyamory.
In W.I.T.C.H., it's actually OT5. There are a few ships with just two, or three of them, but considering certain scenes◊ and artwork◊, it's not hard to see why Polyguardianship has its fans.
◊ and artwork
