I also think season 2 is underrated.
that season had a special tone to it- they tried to make the station more lively, detailed and colorful, like some new alien race member was walking the promenade every episode, new shops etc. DS9 finally felt like a friendly place. this is especially evident in episodes like "Rivals". I mean I liked the dark, almost western-like tone of season one as well. But season two showed that it can work either way. And little fun things like the Cardie Voles, the Klingon chef (hilarious!)and others was what I always wanted to see in Star Trek.
Oh and I love "the Maquis", too. The interaction between Sisko and his old Buddy Hudson was awesome.
I also love how they cared for the details, like including many aliens among the colonists (I think even a Klingon).
I wasn't so thrilled about the "the circle" 3 parter, though. It was very obvious from the beginning that everything would be back to normal. And Li Nalas had "Dead Man Walking" written all over his face.
"The Siege" was especially disappointing. It was just your normal "the station/ship gets taken over and the crew conquer it back" episode. And Li Nalas jumping into the way to get shot was so cliché, so obvious, it didn't touch me.
What I liked about "the Siege", however, was
- Kira and Dax forming a kickass team
- a few nice special effects (but too few overall).
I would say this might have worked better as a two-parter, but for a 2nd season opener (compare with "the child" or *shudder* "Shockwave 2"

), it was pure gold.
Necessary Evil was a surprisingly strong episode. Seeing Terok nor under the occupation was disturbing, and the flashback concept was put to good use.
A few weaker episodes here and there, but quite solid all of them. i also liked how the "secret of the Gamma Quadrant" was subtly hinted at, to be fully revealed with a bang in the (great) season finale.
Paradise was also very good, and Sanctuary had a memorable moment of retconning the Universal Translators, a monument how DS9 so carefully handled the canon and regarded canon as a strength rather than a burden- another example of this is of course "Blood Oath"- pure Star Trek awesomeness

.
I don't wanna spoil "Tribunal", but that was a missed chance at a superb kafka-esque episode. too bad.
But the absolute best thing about DS9's second season is that at the time, TNG was still running.
The (imo) two best Star Trek series pumping out new episodes every week...hmmmm
Those were good times. The best so far. Now that we are actually looking forward to this reboot travesty called ST XI, it looks like this was centuries ago

.