I think their relationship changed and became physically intimate after (big shock here!) "The Impossible Planet/The Satan Pit." What they went through in that episode, before and after the separation, brought them to a new level, I think. First the "stuck with you" conversation. Yes, they were a little awkward and not quite saying what they meant, but it was obvious what was at the heart of their dialogue, and both were clearly thinking in the same direction. For Rose, it's not that big a leap that she could deal with them being stuck in one place, but the fact that the Doctor wasn't freaking out, but came across as in almost the same place as she? That was a huge sign, that as much as he loves the TARDIS and his life as a Time Traveler, being with Rose is enough that he's willing to even contemplate it.
After the separation, we had the first time the Doctor said "I love you," without saying it and then claimed belief in her over any and everything in the entire universe. For Rose, we had her insistence in not leaving, even if he was gone. She didn't care; she wanted to be wherever he was, even if it was just the memory of the last place he'd been. Emotionally, they both took giant leaps here, so a sexual relationship coming off the heels of that two-parter makes perfect sense. And after that episode, these are the little moments we got that led me to believe that, yes, they DID take that step.
- In "Fear Her," a small (if disgusting) thing, true, but the fact that (a) the Doctor casually, calmly holds out his hand, casually and calmly *expecting* Rose to spit chewed up gum into his hand, and (b) that Rose casually and calmly spits said chewed up gum into his hand. I mean, come on? Yes, they are very close. They are, but I couldn't imagine Donna doing that unless she really, really, really, REALLY had to ... and in this case, Rose didn't even have to one "really" have to do it. Yet, it was just a casual intimate moment between them that bespoke of her saliva being on his body not an uncommon occurrence.
- Cheating a bit, I know as it was a deleted scene, but in "Army of Ghosts," as the Doctor and Rose head towards Powell Estate (I assume), they simply hold hands. No rush, no emergency, no danger, no running from or towards danger. They're just two people in love walking along ... holding hands. I know that doesn't say "THEY ARE HAVING SEX!!!OMG!!!!," but tied in with everything else and the fact that it's such a casual, comfortable thing adds to the whole theory.
- One of the biggies ... "Doomsday." Anyone reading this knows exactly where I'm going here.
- Doctor: You've still got Mr. Mickey, then?
Rose: There's five of us now. Mum, dad, Mickey ... and the baby.
Doctor: (Slightly stunned) You're not ...?
Rose: No. (Laughing) It's mum.
Of course, there's another interpretation as the comment came on the heels of "Well, you've still got Mr. Mickey then," but I can't imagine that a few weeks after he and Rose are cruelly separated that he would (a) automatically assume that she got it on with Mickey (or any other guy), (b) not be more than stunned, but rather peeved, annoyed, jealous, etc. This *IS* the Doctor about ROSE!.
So, no, I don't buy that he thought it was Mickey's. That would have garnered a different reaction from the Doctor, indeed. Instead, we got one of slightly being stunned and vaguely wistful response to Rose then giving him that look, before laughing. The dialogue and reactions from both the Doctor and Rose are too telling, in my opinion. And the fact that quite a few people did wonder if it was implying what they thought they possibly couldn't be implying ... which tells me it's quite likely that Rusty was cackling his evil laugh somewhere in glee knowing that people were thinking it. AND being the total Doctor/Rose OTP-shipper that he is, I can't help but think that he *did* intend for people to think that, knowing that they'd dismiss it because it's Who.
- Rose's top in the TARDIS console room in "The Runaway Bride." Yes, the point was that it was supposed to show Donna that there had been another female there giving rise to her kidnapping women fear, and keep the Dotor's angst alive and kicking. But ... her top? Why not a hoodie, or a brush, or some other female accoutrement that didn't scream, 'Hi! I undress in the TARDIS console room where the Doctor and I shag like bunnies!' Okay, okay, fine it doesn't scream that ... BUT, her top?!?! You don't leave your top casually slung about (other than in your bedroom) when you live with someone you don't have an intimate relationship with. So why would Rose's TOP be casually laying about the console room like that unless either she or the Doctor had pulled it off before shagging like bunnies?!?!?! See, just another small piece that fits.
- The choice of phrase the Doctor describes his relationship with Rose as to Martha in "Smith and Jones" when she asks him about who he travels with. It starts out described in a removed fashion as "guests" before rambling into a much more intimate comment about Rose specifically.
- Martha: Is there a crew, like a navigator and stuff? Where is everyone?
Doctor: Just me.
Martha: All on your own?
Doctor: Well, sometimes I have guests. I mean, some friends traveling alongside me. I had ... it was recently ... a friend of mine. Rose, her name was. Rose ... and ... we were together.
- Which brings us to "Turn Left" ... we have Rose's reaction to Donna's: "Were you and him ...?" which while wasn't a ringing cry of 'hell yeah!,' neither was it a denial. At all. In fact, I'd go so far as to say that it actually leaned more in the direction of 'yes, we were' as opposed to 'no, it wasn't like that.' If they WEREN'T together (hah! I wasn't even thinking of the above paragraph, but merely trying to come up with another way of saying 'weren't shagging like bunnies,' and my brain automatically filled in "weren't together" -- see!?!?!?), why didn't Rose just do the slight head shake, laugh, look-down in slight wistful, 'no' sigh that would have easily, no ambiguity there, answer that question? You know why? BECAUSE THEY WERE! Uh huh.
It should be noted that of all of the episodes I referenced above to "prove" my theory, all but "Fear Her" was written by Russell T. Davies. Uh huh.
Finally, back to the kiss in "Journey's End," that kiss coming like it did didn't necessarily mean that they hadn't been, well, you know, and thus the surprise and shock of her pulling him to her like that. Simply it implied that the Doctor had never said the words before -- which really wouldn't come as a surprise from Mr. Euphemism-boy ("Does it need saying?" *Oh, Doctor*). After all, they went right into each other's arms, kissing away like they'd had practice -- and it'd been a really long time since Cassandra, and it was, well, Cassandra! so I'm not counting it.
So, unless we are somehow proven elsewise through canon -- though, how that would ever come up now?? -- all of the above signs, along with their general air about each other, says to me that they were indeed "together," shagging like bunnies, pick your euphemism and nothing in canon disputes that belief if you're not inclined against it. Which I'm not.