Okay, I've gone through PoA and PS looking for hugs and arm-grabs. I had a bit of a problem containing myself to just noting down moments where Harry and Hermione had actual physical contact, though. Ah well... For example, when I came across the Impervius scene, I was struck by the fact that Hermione not only figured out that Harry would be blinded by the rain worse than the other players due to having glasses, she also had a spell ready,
and arrived very soon after the team landed. She must have run at top speed to get there so quickly. And yes, I know that Hermione figuring things out and having a spell or other knowledge ready to roll, and to rush off to aid Harry with it is hardly unusual, but...well, that's kind of the point, isn't it?
I also saw one of the earlier incidents of Harry and Hermione communicating with a glance, on page 145 of PoA. But anyway, I need to get to the point of my search...
In Philosopher's Stone (I refuse to call it Sorcerer's Stone even if that's its title over in my country), there isn't all that much, in the end: the bits with contact between H/HR are as follows:
1. When Hermione grabs Harry's wand to use
Alohomora on the forbidden door, page 160. Just a note: didn't Ollivander say that using someone else's wand was bad for your spell-casting?
2. When Harry goes and tries to drag Hermione away from the troll. He then decides the thing to do is really to
jump on the troll's back and stick his wand up its nose (amazing the way our Harry's brain works, isn't it?). Pages 175-176.
3. The big hug and speech we all know and love so well. No additional comments needed. (Friendship, bravery, and...what?)
4. This is not a moment of actual contact, but I'm mentioning it because it shows Hermione's caring anyway: she
wants to go hug Harry on page 301, but holds off, for which he is grateful because his head's sore. Does anyone here doubt that she knew that his head hurt and that's why she restrained herself?
Although I haven't checked CoS yet, as I recall the book where Hermione starts the whole "grab Harry whenever there's danger" thing in PoA, which I will go on to now.
The first note to make is that there are two occasions, on pages 84 and 339, where Hermione and Ron both grab Harry, for purposes of either helping him up (post-Dementor attack, pg 84) or restraining him (pg 339). There are also a couple of times when Harry or Hermione grab the other, but which IMO are suspicious to hold up as shippy moments due to the fact that they're really, at base, functional: these are on pages 416 (Hermione tugs on Harry's sleeve to remind him that they have to get to the hospital wing), page 417 (Harry grabs Hermione's wrist and they tear into a side room to hide from Peeve; granted it wasn't entirely necessary for Harry to grab Hermione there), page 394 (Hermione grabs Harry and drags him into a broom closet to tell him about the Time Turner. And yes, I am aware that "Hermione grabs Harry and drags him into a broom closet to" could have a decidedly different reason and conclusion, but let's not go there right now), and page 405 (another "restraining" grab, by Hermione alone this time, keeping Harry from running out into the open).
The big thing is, however, pretty much every time Hermione's afraid in PoA and she's within reach of Harry she grabs on to him. On page 160, when they spot the Fat Lady's portrait all slashed up, this occurs: A pretty simple ‘“Oh my—” Hermione grabbed Harry’s arm.’ Of course, we’re never told how long it was before she let go…could it have been until all the students were shepherded into the Great Hall? I consider it possible.
Then, during the business outside and in the Shrieking Shack, there are a pair of very nice little arm-grabs:
1. Page 336, Hermione clutches Harry's arm after Crookshanks freezes the Whomping Willow.
2. She then lets go exactly long enough for them to run down a narrow tunnel and arrive in the Shack, at which point, on page 337, she grabs on again as she realizes where they are. She continues holding until, two short pieces of dialogue and two look-arounds later (I'd say about ten or twelve seconds), on page 338, her grip intensifies to the point where Harry loses feeling in his arm. He raises his eyebrows at her and she lets go.
A final bit, which may go under the "functional" list, is when Harry, on page 413, that Hermione had "better hold on" to him, just after giving her "a leg up". Of course, we're never told whether Sirius was holding on to Hermione when he got on behind her...and Hermione was holding on to Harry "very tight"... Well.
In fairness, on page 292, Hermione hugs Ron and breaks down, after he determinedly (well, exact word was "fiercely") says he'll work on Buckbeak's appeal.
Oh yes, nearly forgot: on page 295, Harry and Ron find Hermione asleep at a table, using her Arithmancy book as a pillow. They both sit down next to her, and Harry prods her awake. I still think this whole scene is one of the cutest Trio moments. From the Harmony perspective, it's interesting that Harry is the one who wakes her up, and the fact that he "prodded", instead of "poked". Could just be the vast vocabulary of JK, but there is a bit of a difference in what images the two words convey, at least to me (note that Dobby "pokes" Harry awake).
Incidentally, amongst all the happiness that this search gave me, there was one bad moment, on page 420 of PoA. It was a line I'd seen and recognized before, but this time it gave me a terrible chilling feeling. Observe, as Fudge has a Aragorn-to-Gandalf-pre-Moria type moment with Dumbledore:
'"Fellow seems quite unbalanced," said Fudge, staring after him. "I'd watch out for [Snape] if I were you, Dumbledore."'
Brrr...
Oh, and....LESS THAN TWELVE HOURS TO GO!!! Time for another freak-out period, excuse me...