Nate's Theme is the actual de facto theme of the series (used in every installment save A Thief's End; although a remixed version is played during the opening credits). Pure adventure in music form.
The City's Secret, from the eponymous chapter, uses wind and string instruments beautifully to portray a melancholy, soft mood. It also shares a melody with the music played over exposition of Marco Polo, giving it some degree of gravitas.
Reunion is a simultaneously tragic and triumphant piece that plays during Schafer's death, symbolizing both Drake's sadness and his desire to push on and take the fight to Lazarevic.
Nate's Theme returns... not as the main menu song, mind you, (the menu is silent) but as the opening and closing credits song. They somehow made the song even more epic.