When Sora gets to Twilight Town in Chain of Memories the following dialogue occurs (courtesy of The Forgotten One's post in the "KH:COM to KH2" thread):
"Sora: No...it's different. With Naminé, the memories of us together sort of came drifting back piece by piece. But here, there are no memories. Everything feels familiar, that's all.
Vexen: Does it, now? (appearing) A question, then, Sora... Which is more real to you: your memories of Naminé, or the familiarity you feel here?
Sora: Naminé, of course! Whatever I feel here is just some trick of yours!
Vexen: Ha ha ha... The memory's wiles are cruel. In its silence, we forget. And in its perversion, it binds our hearts firmly.
Sora: I don't have time for your riddles!
Vexen: Then recall that this place was made from another side of your memory. Yes, the other side of your heart knows this place. The other side remembers.
Sora: You're wrong! I don't know this place!
Vexen: If you remain bound by the chains of memory, and refuse to believe your heart...then you may as well throw your heart away."
I think that if we assume that the BHK is to Sora as Naminé is to Kairi (at one point in Chain of Memories Naminé says that she is Kairi's shadow [I don't remember the exact words. Anyone?], so the BHK can be Sora's shadow, given the physical resemblance [minus the blonde hair, obviously, but then again Naminé's hair is also blonde, whereas Kairi's is red]), and knowing that the BHK lives in Twilight Town (from the various KH2 trailers and the image at the end of Chain of Memories), we can assume that Twilight Town is the home of everyone's shadow self, and that Naminé was presumably kidnapped from Twilight Town by the Organization.
This in turn could mean that Sora recognized Twilight Town when he gets there because his shadow self lives there, and so part of him, "the other side of your heart" as Vexen says, recognizes Twilight Town, thus causing Sora to have the familiar feeling that he gets.
Make any sense, or am I rambling?