Pathfinder: The first issue has some light flirting between Valeros and Merisiel, the latter of whom even says she isn't in the mood for him at the time but might be at some later date. She ends up starting a relationship with Kyra in issue 6 (they eventually marry in a Short Story on Paizo's blog), which Valeros accepts without complaint when he realizes.
In Scott Pilgrim, any chance of Scott getting back together with Knives was shot down when he tried kissing her after his break-up with Ramona and the kiss was so awful that the narration said it "made everyone feel terrible. Including you", the latter part reading like a Breaking the Fourth Wall jab at readers who were still hoping for a Scott/Knives reunion despite the comic having constantly portrayed Knives' feelings for Scott as an unhealthy obsession over a boy who never liked her all that much that she needed to move on from.
Another one that Ian killed was Sonic/Fiona and Tails/Fiona, the former of which hooked up near the end of Ken Penders' run. Some had theorized that Ken had done so due to the fact that Sonic and Fiona were a couple in a fan comic Ian had done before coming to Archie. Ian promptly sunk it by having Fiona reveal that she only fell in love with him because she thought he'd be the same as his Evil Twin, Evil Sonic (later Scourge). Fiona, then, sunk Tails/Fiona by telling him how gullible he was to think he felt that way about her and backhanded him. Interestingly, Sonic's relationship with Fiona would be a point with a small falling out between Sonic and Tails.
Sonic Universe Issue 58's off-panel◊ takes a jab at Silver/Blaze. Blaze burns Marine's paper, with Marine complaining that she's "sinking her ship".
According to Ian Flynn, years of dealing with the shipping wars lead to him throwing his hands up in the air and ending the Sonic/Sally pairing in the post-Super Genesis Wave universe.
In the early days of W.I.T.C.H., one of the popular pairings was Cornelia and Caleb, which ended up getting sunk after the Nerissa arc with Caleb opting to stay on Kandrakar. Fans were upset at this, especially with a What If? special that proclaimed on no certain terms that the two together would never last. While Cornelia would end up with Taranee's brother later on, the cartoon would keep the two together.