Wow, it took me very long time to think my answer through and I'm still not sure that this is my answer!

I was caught up between season 2 and 3's finale because season 2 had Chuck getting the Intersect 2.0 and using Kung Fu to kick the bad guys' asses and I really loved that, I even recorded the entire episode because of that but the rest of the episode was awesome too, I just remember that best. Season 3 had the final fight between Chuck and Shaw with Jeffster music playing in the background which was hilarious but it was the whole Intersect vs Intersect that fascinated me to the bone so even though I'm still in a doubt... I'm going to say yes, Season 3's final was the most epic!