One of my favorite Hermione characterizations in fanfic is
arsenicjade's
Care of Magical Creatures. I've been meaning to recommend it for forever, but I think I just needed to dwell on it for a while. It's one of those.
Anyway, it's a novel-length, and it's all about personal recovery from the trauma of war, within the context of post-war reconstruction of wizarding society and prejudices -- specifically, hatred of werewolves. There are certain emotional moments in the story which just made me sort of catch my breath in amazement. If you can get past certain Americanisms and some odd stylistic stuff, it's pretty fantastic.
The pairing is Hermione/Remus/Severus (but takes a long and thoroughly decent while to build to it), with Hermione/Ron/Harry in the past. Life has not been kind to these characters. They really broke my heart.