I mentioned it on some comments before, but I think it can make an answer of its own.
I would say that a particular affection was hinted as far back as GoF and the whole Yule Ball thing. But nevertheless it might back then have been something that the characters themselves did not realise. Note that Hermione was somehow expecting Ron to ask her to the ball. Not Harry, with whom she had a closer friendship. And indeed it was Ron who did, albeit too late.
In GoF, the whole Hermione-Krum part is left somehow cloudy in the books. We don't know for certain what has or hasn't happened, but when Ginny replied back at her brother in HBP, she clearly indicates that Hermione was with Krum. Same when later she invites McLaggen, the other Gryffindor girl also mentions that. So we don't know for sure, but there is a possibility that indeed something happened. This is actually more shown in the films with the discussion Harry and Hermione have about it on the Bridge.
Nevertheless the relationship she had (or didn't have) with Krum seemed to be a marker for Hermione to realise the growing feelings she had for Ron.
Interestingly, she was somewhat supportive of Harry's relationship with Cho. But not at all of Ron's with Lavender.
HBP and the whole Lavender thing seems to be a strong indication for me and would count as the first clear sign. When Lavender kissed Ron, somewhat surprisingly for him, she left the place and Harry followed her. She was upset about it. There is the McLaggen thing, where she tried to make Ron jealous. And finally, the hospital scene, when Lavender left Ron, and Hermione stays with him.
Earlier in HBP, she identified the smell of Slughorn's love potion. And she hushed the last one, making it plainly clear that she was conscious of having feelings for someone, later understood to be Ron as e.g.:
Jess Mac: What was the third smell that Hermione smelt in the Amortentia potion in HBP (ie the particular essence of Ron)?
J.K. Rowling: I think it was his hair. Every individual has very distinctive-smelling hair, don't you find?
Some points which might be of interest from DH:
- Ron acquired a book for his 17th birthday and was intent on using what he learned from it to actively seduce Hermione.
- At Bill and Fleur's wedding, they danced together, prompting Krum to ask whether they were together.
- And Hermione's muteness when Ron left.
I don't have the books in paper form, so any quoting is a pain, but I tried to be explicit enough with the scenes.