I'm not really answering the question; it's just a starting point for writing about something that's been on my mind: anti-canon shipping. I've realized that it's very rare for me to ship against canon. By that I mean, if two characters end up together in a story or series I enjoy, I almost never wish for either of them to have ended up with someone else. I've really been racking my brain for examples of this, since it's such a common occurrence among my fellow fans. I can only think of four exceptions, though there may be others I'm forgetting. (You may notice that all of these, save one, were at least canon at one time.)
Oz/Willow on BtVS: These two had a long-running relationship on the show, of course, but the romance went awry, Oz disappeared, and Willow ended up in another relationship or two, first with Tara and then with another girl, I think, who she may have still been with when the show ended. (I stopped watching the show around the fourth season, but my parents still watched it, so I heard things from them.) I just loved Willow and Oz together. I liked Oz for most of the same reasons I like Remus Lupin—smart, funny, gentle, a bit downtrodden, and secretly a
Clark/Chloe on Smallville: I never meant to get attached to this ship, as I knew Clark ultimately had to end up with another girl someday—Clark/Lois is a done deal, right? But I couldn't help empathizing with Chloe's crush and thinking Clark was a dummy for not noticing how cool and beautiful she was and how totally good for him she'd be. He did date her briefly, but most of the time he mooned over Lana—another doomed relationship. But then there came an episode where the writers of Smallville messed with my head: They had Chloe use the name "Lois Lane" as a pseudonym. I took it as a sign that Chloe would eventually become Lois, and jumped headfirst into delusional shipping. Oops! Well, things didn't go the way I hoped, and I've since dumped the show, more for its increasingly convoluted yet somehow boring plot than any shipping factor.
Jake/Nina on Everwood: Mainly, I liked this ship because I think Scott Wolf is adorable and that any girl should want to snuggle him. :) They were together for much of the last season, but Nina chose a different guy in the end—as I knew deep down she would. Oh well. I watched the show to the end, and the lack of the ship I wanted didn't diminish my enjoyment of the series overall. (This reminds me that I also thought Scott Wolf's character on Party of Five should have ended up with his long-time girlfriend on that show, and yet the writers left it ambiguous. That's not really shipping against canon, though—just wishing the writers had given a more definite happy ending. )
Marius/Eponine in Les Miserables: This ship was only ever one-sided at best in canon. In this case I'll have to confess I was influenced by an extremely popular fanfic--one more popular than the original canon, probably: the Broadway musical. True, it was still pretty much one-sided in that as well, but the musical writers did ramp up the appeal of the ship quite a bit. I'm not opposed to Marius/Cosette, mind you, I just found Eponine to be a more interesting character than Cosette, and I could never keep myself from thinking, "What if…"
In addition to these ships, I've also liked some crack ships that were neither confirmed nor contradicted in canon. I'm a romantic, so I like to see characters I like happily paired with someone, and I'll sometimes indulge in searching around for suitable matches between characters who were never involved or interested in each other, and in some cases maybe never even met! Hence I've toyed with the idea of Kagura/Momiji or Kagura/Kunimitsu in Fruits Basket, Ty Lee/Haru in Avatar, Remus Lupin/Hestia Jones in HP (before HBP came out), and others.