These stories all have a serious squick factor, at least for me. I've got a fairly low tolerance for this stuff, so some people will probably find them tame, but I sure didn't. The stories also have redeeming aspects, things that might make the discomfort of reading them worthwhile, which is why I'm putting them here. Let nomination in this category serve as a warning to those with weak stomachs: don't even think of reading these stories.
I don't warn in this blog, but this nominations set is going to be an exception. And I don't cut away in nomination posts, but again, this set is an exception. And I try to be amusing in most of my nominations, but you know what? Exception.
Best FF Look at Those Who Do Nothing and Allow Evil to Triumph: Welcome to Purgatory, by penknife. Horatio Hornblower, Clayton/Kennedy, Kennedy/Simpson, (Clayton/Simpson). Warnings: rape, physical abuse, abuse of power. Kennedy is in hell. But watching him suffer is purgatory. This one is incredible; it gets right into the minds of those who watch, and sympathize, and do nothing. A true jaw-dropper of a story, but painful and sad and very hard to read.
Best FF Featuring Topping from the Bottom: Action, from Principle, by Weirdness Magnet. Batman comics, Batman/Robin. Warnings: non-consensual sex, probable statutory rape. This is the perfect in-character Batman, to me - twisted beyond hope, powerful and helpless at the same time. This story plays with balances of power and does it really, really well.
Best FF with So Many Warnings That They're Practically a Story in Themselves: Border Men, by Janete. Hellblazer X Buffy the Vampire Slayer, John Constantine/Ethan Rayne. Warnings: rape, implied child abuse, enslavement, violent sex. This one's a crossover between two fandoms I know nothing about, so it's possible that a lot of the elements that I found interesting - the magic, the chaos, etc. - are simply imports from the canon. But even if that's true, this story does two difficult things very well. First, it handles sex-between-enemies in a believable way. And, second, an abusive background for a submissive person almost never works. But in this one, it does.
Best FF That Was Both Funny and Nausea-Inducing: A Most Disquieting Tea, by Telanu. Harry Potter, Harry/Snape. Warnings: implied pedophilia. Why does Snape treat Harry so badly? Maybe because the alternative is even worse. There's nothing explicit at all in this story. It'd be PG if the underlying concept wasn't so squicky. The author does a remarkable job of writing to the canon, and both Snape and Dumbledore are perfectly in character here, and this is an excellent answer to an often-posed question.