Ok, I'll start with the bad bits so I can wax eloquent about the really, really good bits afterwards: Jeffster. Please spare me. While Jeff and Lester can be great fun at times, I found the whole scene distasteful, unfunny and malapropos (as in: it stuck out like a sore thumb and didn't fit into the flow of the show).
The birth - not THAT bad, just your average unrealistic TV birth. ;) Although I guess Chuck isn't the sort of show I watch for realistic injuries and believable birthscenes anyway. The great bits:
Chuck out-agenting (yes, I made up this word) Sarah and Mommy Dearest. Brilliant - he had a plan and he followed through; just like Brian Boitano'd do. :D
It was great to see him coming into his own, planning, executing a complex plan and doing an excellent acting job without any visible signs of nervousness; the Chuck of old would have stuttered and sweated bullets.
I really loved it when he opened the door, doing the "coolly understated" thing with his "Will this suffice?" - two thumbs up, Chuck!
The Proposal - which was just perfect, a wonderfully impulsive and unchoreographed move that was Just Right, and I LOVED that they zoomed out and muted the sound, giving us a glimpse of this very private moment but not doing any invasive closeups. Minor bits of absolute loveliness/coolness/funniness:
Casey and Alex, admitting and affirming their growing bond as father and daugher - short and sweeeet. Captain Awesome totally losing his cool in the heat of the moment, and the übercool response team summoned by his desperate text. All in all a very good episode, despite a few scenes that I felt fitted badly with the overall smooth flow of the story.
It's interesting to see how Chuck has grown throughout the series, both as a character and as the actor behind it; Chuck Bartowski, in the body of Zachary Levi, has gone from overgrown puppyish boy to a mature young man, and it's been a good, steady progression, a believable, growing maturity.
Well done, people - I'd say you made a REALLY good casting choice back when. :D