I've read so many fanfics about Harmione/Harmony and many are really, really good! My absolute favorite at this point is one called Always and Forever by a fan named Neiva.
At it's core it's about how Harry and Hermione fall in love with each other and ultimately end up having an affair behind Ron's back. It does a really great job of highlighting the intense connection Harry and Hermione have and displays it in a really unique way. Unfortunately it's an unfinished chapter fic, but everything up until the end is really great!
I read as many Harmony fanfics as I can get my hands on, so who knows if a new favorite will arise in time.
Not one has captured my eye. I want to make a new one between the time in Deathly Hallows when Ron leaves and comes back. I'll have Harry & Hermione realize they love each other and make them do things like dancing and comforting each other. There's going to be a big standoff about who says, "I like you," first. In the end, they say it to each other at the same time and then hug. Ron comes back just when they hug and starts to leave because he's jealous. Hermione and Harry say that it isn't what it seems and then Harry and Ron get into another big fight. I have nothing after that. I want to make a new fanfiction, but I'm waaay too lazy.
I don't know, read so many.
I have a favourite, but read it once and haven't found it again :( , but out of the ones that I know i really like The Living Dead ( fanfiction.net) I don't know why but it's awesome :)