Seed -
Destruction of Heliopolis - that scene, coupled with the 1st ender, was really powerful
Nicol/Tolle's deaths - yeah...everything changed with that. Seed Destiny 29 reminded how "o\/\/n3d" Tolle was
Rau's speech - when I saw this, I got chills. A storm was in his voice and it was on its way (Seed Destiny)

Seed Destiny -
The Fall of Junius 7 - I cried out of sheer emotion when "Reason" started playing and we see Kira for the first time since Seed... that screams to the audience that it's begun.
Broken Bonds - Shinn vs. Kira, Kira vs. Athrun redux, ORB vs. ZAFT, Shinn/Athrun vs. Auel/Sting: all in #28. All around the best episode of the series so far.
War is Peace - Gilbert's speech about power and how it is necessary. George Orwell would be proud, lol