I think everyone ships Two/jamie, they are just so, er shippable, and so very slashy. FIVE/TURLOUGH (as well you know!) Peri/Erimem to an extent... really not enough fic round for that :( I'd say Six/Peri is cute, but I can't see anything actually happening between them. Ace/Hex OBV, pretty much canon as well, Eight/Fitz, (even though I've never read the guy) Eight/Charley, Ten/Rose, Jack/anyone (I read one fic of Jack/Peri!) Five/Ten/Eight any mixture of (As you can guess, I'm a bit of a slave to the pretty doctors), and I haven't really seen any Torchwood, but sure, we can count it and other spin offs.

the asexual!Who people would hate me...
all the more reason to ship my dear ;)