I know nobody believes me when I say they're actually dating by OotP, but I think they are...
Starting in PoA, and especially in GoF and OotP, Hermione and Ron spend a lot of time together without Harry around.
Ron's reaction when he hears about Harry's first kiss cracks me up... and makes me think he's somehow comparing it to his first kiss... who else would he be kissing but Hermione?
In GoF, when Harry and Ron aren't speaking to each other, Hermione is obviously spending a lot of time with each of them seperately. Also, when she is going to spend the day at Hogsmeade with Harry, he's suprized, assuming she'd want to spend the Hogsmeade day with Ron. Why would he make that assumption unless he's already realized there's something there between them?
In OotP, the thing that upsets Harry the most at the beginning is that Hermione and Ron are together. We know they are, and that they're spending time together, but they also apparently confide in each other, argue over what's best for Harry, and do some amount of consoling each other (well, the consoling comes later, when Harry takes out his feelings on Ron and Hermione, Ron steps up and speaks for himself and Hermione).
In OotP, I don't think it's that they're dating and trying to keep it a secret... I think it's just a given by that time. Harry knows it's there, but since so much is going on in Harry's life, they try to play it down to keep from adding the third-wheel feeling to his other problems.