Best parts (in my opinion) of each track are...

Where the Dream Takes You-No special part in particular
The Submarine-Beginning to 0:22, 2:16 to the end
Milo's Turned Down-Nothing in particuar
Atlantis is Waiting-Beginning to 0:21, 1:12 to 1:47, 2:13 to 2:25
The Leviathan-Beginning to 1:10, but the whole thing still rocks!
Bedding Down-No special part
The Journey-Beginning to 0:11, 0:51 to 1:27, 1:41 to the end pretty much
Fireflies-No special part
Milo Meets Kida-Beginning to 1:05
The City of Atlantis-0:47 to 1:18, 1:40 to 2:07
Milo and Kida's Questions-1:09 to 2:26
Touring the City-0:21 to 1:41
The Secret Swim-Definetly 0:30 to the end
The Crystal Chamber-0:57 to the end
The King Dies\Going after Rourke-Nothing in particular
Just Do It-0:59 to end
Kida Returns-0:39 to 1:20
Atlantis-0:53 to the end

I'm not suggesting anyone should ONLY listen to those parts, or that those are the ONLY good parts!!! I was just noting the particular section of each track that I enjoyed.

Finally, my favorite two parts of the soundtrack (if you didn't pay attention to the above, at least try out these sections please!) :
The City of Atlantis-1:05 to 1:18
the Secret Swim-0:33 to 0:56

I would love to hear people's favorite sections to give me some comments please! Elly

Well, after reading your comment I thought I'd go try out the sections you outlined...
I ADORE The Secret Swim as well. It is the most worn-out section on my CD!