Oh, wow. I really can't think of one section in particular that strikes me as epic. Like you said, it brings out so many emotions throughout.
The one I'll have to name, while not epic in the sense of guns-a-blazing action, is when you leave Robo to plant Fiona's forest in 600 A.D.. The way it unfolds where you just drop him off, hop in the epoch, plow through time, and then re-emerge ~400 years later to pick him up really encapsulated the magnitude of time and put its power into pespective for me.
While I cant remember Robo's exact quote, I know it was something to the tune of 'it was just a short trip for you, but for me it was four-hundred long years.'
While the Chrono series firmly established my attachment to the theme of Time (one look at my house will proove this), this scene in particular emphasises it.