Honestly, I can't pick one arc of this show that's my favorite. The mutiny arc in Blood on the Scales is one of my favorites, especially since *SPOILER SPOILER SPOILER* Zarek is a character that really intrigued me throughout the show, and I wanted to see him in action since Bastille Day, but the completion of Gaeta's tragedy is what I love. His trusting nature, his willingness to put faith in leaders that inspire change, also shown with Baltar on New Caprica, ended up being his downfall. Watching his reaction as he realizes that it's all spiraling out of control when Zarek murders the Quorom, oh man.*END SPOILER, BUT WATCH OUT, I'M GONNA BRING UP A FEW MORE. LIKE NEXT PARAGRAPH*.
The New Caprica arc takes the cake for me, though. That entire arc. From seeing our favorite characters as terrorists, to the night time kidnapping scene, to the EPIC finish, it had me gripped from start to finish. Gotta give a shout out to the *SPOILER* reveal of the Final Five. For days after watching that episode, I was in disbelief. *ENDSPOILER*