For me, it's actually pretty rare that I'll ship anything that's canon. Part of this comes from the fact that most of my ships are slash. And part of it is that I don't like the show trying to tell me who I should be shipping.

There are some canon ships I really love, though. Claudia/Fargo, Zoe/Wash, Willow/Oz are the only ones I can think of at the moment... (ETA: Oh, and Peter/Elizabeth from White Collar, though I really OT3 Peter/El/Neal...)

(I AM RAMBLING. Sorry. I'm a little tipsy, and am writing fanfic FOR A SHOW THAT DOESN'T ACTUALLY EXIST. One that I wrote, in fact, so I'm not even sure if it's fanfic or just a really fleshed-out portion of script. XD And for some reason this is making me REALLY TALKY.)