"Secret" Dialogue
So I'm doing my playthrough with the hidden blade only, and I noticed something.
When going to cities to do your investigations, you have to speak with the bureau leaders. If you lock onto them after they've told you where you need to go, they'll say something sarcastic and ask you to leave their bureau. If you continue to lock onto them you'll eventually get a different line of dialogue each time you lock on. Just keep locking on and you'll see (sometimes they will repeat the same line before you get to a new one). For example at the bureau in Acre, I counted 6 or 7 different lines that the leader said to me before I got bored and left.
And I noticed another thing. If you return to the bureau while in the middle of your investigations, it will trigger a cutscene with even more dialogue, and afterwards you can lock on again and you can hear a few more different lines.
I'm not sure if anyone's noticed this yet, but I thought I'd share because this "secret" dialogue really gives the bureau leaders more personality.
Oh yeah, I remember these. I never stuck around to hear all of them, though. These added more depth to those characters and was something of a prize for players that enjoyed exploring more than most.
Synch was kind enough to write down all the dialogue a while back.
http://thehiddenblade.com/harassing-rafiks
EDIT: There's also variations in the dialogue right before the assassination, possibly based on whether you did all the investigations or some other factor. Here's an example in the memory block 6 Jerusalem assassination:
https://youtu.be/ahPg7RQ9sNU?t=1290
https://youtu.be/itkIK95xBWI?t=1368
I'm really glad someone actually took the time to write all that down, I was actually going to record everything and post it on here if no one had done it already.
From watching those videos, it appears that you're probably right in that the dialogue changes depending on how many investigations you do. I have finals this week, but if I can find time I'll test out that theory out and see what I can find.
These added more depth to those characters and was something of a prize for players that enjoyed exploring more than most.
Little touches like this are one of the many reasons I love AC so much. For example in AC2 I always loved seeing the different facial expressions Ezio made after missions or when talking to someone he knows during an escort mission. It's one thing to do that stuff in a cutscene, but another to do it in-game when not everyone will notice it.
And on the other side of the coin even though there is so much attention to detail, all the assassins in AC1 except Altair still had all their fingers.... lol
In AC2 you can eavesdrop on a side conversation during the Marco Barbarigo assassination. Ian called it the "other brother":
http://www.thehiddenblade.com/marco-barbarigo-assassination-variety-pack...
I was actually going to record everything and post it on here if no one had done it already.I have finals this week, but if I can find time I'll test out that theory out and see what I can find.
Any recordings are appreciated. 
Malik was the only one I noticed there being any different dialogue with.
In AC2 you can eavesdrop on a side conversation during the Marco Barbarigo assassination. Ian called it the "other brother":
http://www.thehiddenblade.com/marco-barbarigo-assassination-variety-pack-part-2
I actually already came across that post, I tried to replicate one of the assassinations and failed so badly it was embarrassing!! Totally didn't realize that "the other brother" was the guy in the cutscene with Antonio though.
Any recordings are appreciated.
Well I can certainly make some recordings then! I can't promise I'll get to it anytime soon though, I've never used a capturing program before and I'm too busy right now. But I'll have a lot of time on my hands this summer, so I'll try to eventually record every bit of extra dialogue I can find.
I remembered there was one conversation where Altair says something you can't hear. Now I found it.
Right before the Sibrand assassination, if you don't do all the investigations, near the end of the conversation the Rafik says, "Let Al Mualim's will be done." Altair then moves his mouth with no words coming out, and right after the Rafik says something else.
Now if you do all the investigations the Rafik instead says, "be on your guard, Altair." Altair ends the conversation by saying, "of course, Rafik. But this will be to my advantage. Fear will weaken him."
So the wordless dialogue might actually be recycled from the other variation of the conversation that the devs forgot to remove. The only way to know for sure is to play a side by side comparison to see if the mouth movements are exactly the same.