Just did a compressed "greatest hits of S2" viewing consisting of 3 episodes - Vs the First Date, Vs Santa Clause, and Vs the Colonel.
Chuck Vs the First Date is, to me (with S1's Vs the Tango coming in a very close second), the episode I would show anyone if I had but one episode to show them to get them hooked on the show. There are better episodes in the series (although not too many!) obviously, but most of them are too deep into the major arcs to be fair game to drop someone into without prior knowledge. This one really has all the classics elements firing on all cylinders. The A plot is really fun and ties in nicely with the overarching mythology, its very funny and charming, it features some great Chuck and Sarah (before Chuck and Sarah became a bad thing), and has a fun guest appearance. On top of that, it does a very brief recap of S1 for the uninitiated.
Chuck Vs Santa Clause is the perfect example of the incredible balancing act between levity and gravitas that the show has been capable of at its finest moments. For the first 30 minutes or so of the episode its a rather light hearted, comical and downright silly hostage plot/Die Hard homage, but then out of nowhere it takes a distinct turn into a dark area and suddenly becomes very weighty when we witness Sarah murder a Fulcrum member in cold blood to protect Chuck. I for one love when the show has displayed that darker edge and a sense that there are indeed stakes and danger in the world of Chuck. Also, the scene in question is probably the creepiest thing in the series. There is something downright eerie about two killers stalking eachother amidst rows of Christmas trees while Silent Night plays.
As for Chuck Vs the Colonel, nothing has changed here so I won't say much - subjectively, its my favorite episode of the series. Objectively, I would call it the best episode of the series. When Chuck's father removes the intersect is a moment of great catharsis that had been building for two seasons which gets me every time.