While I really like Season 2 overall, because I like the Swan Station setting and the introductions of Desmond, Ben (a.k.a. Henry Gale), and The Others, not many episodes stand out as exceptional enough to be all-time favorites.
Season 2 - Favorite
[2.07] The Other 48 Days
Season 2 - Honorable Mentions
[2.04] Everybody Hates Hugo
[2.05] ...And Found
[2.16] The Whole Truth
I like "The Other 48 Days" the best out of Season 2 because it shows us something completely different -- what happened to the people in the tail section. We see that there were actually several survivors. Some were abducted by The Others, including the kids. We're introduced to whole new set of characters: Ana Lucia, Libby, Mr. Eko, Rose's husband Bernard, and the flight attendant Cindy. Considering that Ana Lucia, Libby, and Eko all get killed, Cindy joins the Others, and Bernard eventually "retires" with Rose, the tail section story doesn't really add much in the grand scheme of things, but it's an interesting diversion, especially considering how it's woven so intelligently into the main storyline with the Tailies finding Sawyer, Michael, and Jin after the raft explosion.
I like "Everybody Hates Hugo" because it focuses on one of my favorite characters, Hurley. It begins with a dream sequence in which he's speaking Korean, and Jin, standing beside a guy in a chicken outfit, speaks perfect English. Later, we see what happens when Hurley wins the lottery and how it affects his responsibility in rationing the Swan Station food stash. Many of my favorite scenes in Lost are the "music montages" in which emotional music plays over a scene without dialogue. They're occasionally done in slight slow motion and usually involve departures, reunions, mourning, celebration, etc. The music montage in this episode is Hurley giving out *all* of the food to the entire group of survivors in one night, which brightens everyone's mood and basically turns a normal night on the island into a party. It's one of Hurley's finest moments.
I like "...And Found" and "The Whole Truth" simply because they focus on Sun & Jin who are always interesting characters to learn more about, even when they're story doesn't seem that important in the grand scheme of things. "Lockdown" is good because we get to see the map drawn in invisible ink on the Swan Station blast door and see some interesting interactions between Locke and Ben. "S.O.S." is unique because it's the only Bernard & Rose -centric episode.