The TARDIS! (duh…)
Oh wait - you mean that other kind of ship. My bad.
I'm not really one for shipping, honestly. I usually just go with whatever's established in canon - that way I don't get eaten by the rabid-shipper-people (even then I'm not 100% safe). But I think that Sally Sparrow and Larry Nightingale from "Blink" are particularly adorable.
Wouldn't it have been cool to have Sally and Larry on board the TARDIS, though? Yet another instance of What Could Have Been (in my head, anyway).