Best: "Chuck Vs. The Santa Suit"
A lot of good concept shows are plot first, characters second. Therefore it was a relief that Chuck took its time to let its characters naturally grow into their destinies. The plan was always for Chuck Bartowski to become a real-deal spy, but in retrospect it's admirable that Fedak and Schwartz let his evolution marinate over the better part of three seasons.
Over time we came to realize that it wasn't the Intersect that made Chuck a worthwile spy, and it all came to a head this season in the series highlight "Chuck vs. the Santa Suit," in which he squared off with nemesis Daniel Shaw (Brandon Routh) and saved the day all on his own without the super-computer crutch, completing a five-year transition from geek to hero. (The episode also confirmed, as we all assumed, that Stan Lee does indeed work for the CIA.)