Nothing too important...

1) Right after Sherlock makes the deduction about Mrs. H. and Mr. Chatterjee and she storms out:
John: What the bloody hell was all that about?
Sherlock: I don't understand.
John: Go after her and apologise.
Sherlock: Apologise?
John: Mm-hmm.
Sherlock: Ah, John, I envy you so much.
John: You envy me.
Sherlock: Your mind is so placid, straightforward, barely used. Mine's like an engine, racing out of control. A rocket, tearing itself to pieces, trapped on the launch pad. I need a case!
John: You've just solved one! By harpooning a dead pig, apparently.
Sherlock: Ah, that was this morning. When's the next one?

2) After meeting Frankland for the first time, the tour continues:
John: So what exactly is it that you do here?
Corporal: I thought you'd know, sir. This being an inspection.
John: Well, I'm not an expert, am I?
Corporal: Everything from stem cell research to trying to cure the common cold, sir.
John: But mostly weaponry?
Corporal: Of one sort or another, yes.
John: Biological, chemical . . .
Corporal: One war ends, another begins, sir. New enemies to fight. We have to be prepared.

3) As John and Sherlock are driving away from Baskerville after their first visit:
John: So - the e-mail from Kirsty. The missing luminous rabbit.
Sherlock: Kirsty Stapleton. Whose mother specialises in genetic manipulation.
John: She made her daughter's rabbit glow in the dark.
Sherlock: Probably a fluorescent gene. Removed and spliced into the specimen. Simple enough these days.
John: So. . . .
Sherlock: So we know that Dr. Stapleton performs secret genetic experiments on animals. The question is: has she been working on something deadlier than a rabbit?
John: To be fair, that is quite a wide field.

4) After their first trip out onto the moors with Henry, after Sherlock says he didn't see anything, and before the scene with Sherlock and John in the pub, we see John taking Henry back to his house:
Henry: He must have seen it. I saw it. He must have. He MUST have. Why? Why? Why would he say that? It was there. It WAS.
John: Henry - Henry - I need you to sit down. Try and relax. Listen, I'm going to give you something to help you sleep, alright?
Henry: This is good news, John. It's - it's - it's good. I'm not crazy. There is a hound, there - there is - and Sherlock, he saw it too. No matter what he says, he saw it.

5) After John leaves the pub, having been told Sherlock has no friends, we miss a scene of Henry, restless, having flashbacks to when his father died.

6) After John and Sherlock drive through the gate into Baskerville for the second time, there's a scene between Sherlock and Major Barrymore:
Barrymore: Oh, you know I'd love to. I'd love to give you unlimited access to this place. Why not?
Sherlock: It's a simple enough request, Major.
Barrymore: I've never heard of anything so bizarre.
Sherlock: You're to give me twenty-four hours. It's what I've . . . negotiated.
Barrymore: Not a second more. I may have to comply with this order, but I don't have to like it. I don't know what the hell you expect to find here, anyway.
Sherlock: Perhaps the truth.
Barrymore: About what? Oh, I see. The big coat should have told me. You're one of the conspiracy lot, aren't you? Well then, go ahead, seek them out. The monsters, the death rays, the aliens.
Sherlock: Have you got any of those? Oh, just wondering.
Barrymore: A couple. Crash-landed here in the sixties. We call them Abbot and Costello. Good luck, Mr. Holmes.