When the gang stages an intervention over Marshall's hat on How I Met Your Mother. While the hat did remind me of The Cat in the Hat, I had never actually read any of Dr. Seuss' books, so when Robin started rhyming, I found it quirky but didn't get the reference.
Quite some time later, I somehow ended up reading parts of Green Eggs and Ham on Wikipedia or something out of boredom. A few days later, I catch the episode on television, and suddenly the scene was much funnier. I have since watched it with two other people, and have had to explain why it's so funny both times.
But yeah, Arrested Development is the king of repeat viewings, though I'm sure everyone already knows that. I also quite like watching old episodes of The Simpsons, as I often find myself getting jokes that I missed when I was younger or catching subtler jokes.