*thinks*

Blood Magic--there are 'ships, slash ones. Threw me, too, but I didn't find it terribly distracting. The father-son dynamic is so well-written.

In Blood Only--none that I can recall

AYLNO--no ships, at least none that are central enough for me to remember, it's so freaking epic and it was such a long time ago... But again, who cares, it's ridiculously good

Resonance--lots of random Harry ships. It's part of his character though--he's not well-adjusted enough in this fic for normal relationships. Snape has a very well-developed plot arc with an OFC

Battle of Wills- don't remember...

Go with the Tide--nothing till the end

I will say that none of these ships interfered too much with my reading, though. They're all good strong fics :)