I'm the kind of shipper where - as long as Spike/Buffy are together, I kind of don't care who the others pair up with.
Most of my fandom interaction is through fic, so that's what I'm talking about here, lol.
But yeah, the 'secondary' (to the ship I'm interested in reading about) have never really mattered to me.
That said, I've enjoyed reading Giles/Anya as a secondary ship (I don't think this could be considered canon based on one kiss, right?). Um, I've read some Faith/Buffy fic and though I'm not really into slash or femmeslash, the author made it work.
But the non-canon ship I enjoyed the most is Spike/Tara. Which might be surprising considering I'm a Spuffy shipper, but the few Spara fics I've read made it work surprisingly well.