I think that in many cases, the second season of a TV show is its best season. Why is TV so often completely opposite from sophomore efforts in music and movies? From my own observations it's because in the second season of a TV show, the actors have gained a comfortable grasp on how to portray the deeper parts of their character. At the same time, the show still has the freshness of a new show, the same rich texture that won it a debut to begin with; the writers are still developing plots that don't feel stale, so the show hasn't lost that "new car smell". Of course there are exceptions: shows that run out of steam soon after they start, and shows that just seem to keep getting better even after the second season.
I don't know if The West Wing's second season is its best, but it definitely includes some of the best episodes. Great writing, great acting, great sets and music, all come together to form what has become my favorite TV show ever.
Season Two includes these episodes:
In The Shadow of Two Gunmen (Part 1)
In The Shadow of Two Gunmen (Part 2)
In This White House
And It's Surely To Their Credit
The Lame Duck Congress
The Portland Trip
The Leadership Breakfast
The Drop In
Bartlet's Third State of the Union
The War at Home
Somebody's Going to Emergency, Somebody's Going to Jail
The Stackhouse Filibuster
Bad Moon Rising
The Fall's Gonna Kill You
18th and Potomac
(You can look up an episode guide if you want a quick summary of the plots; I didn't want to spoil any surprises here.)
I doubt Warner will include the special episode "Isaac and Ishmael" in this set. This episode was written after the 9/11 attacks, and aired a week before the start of Season Three; thus, if it is included with a regular season, it will probably be the third.