I really like season 2 overall. I think it's a lot better than season 1 or the later seasons.
In fact I'd probably put it right behind season 3 and 4 as far as my overall favorites. The highs are really high, and there's only a few lows that are really low. (outrageous okona, shades of gray, up the long ladder, the child i'm lookin at you)
Matter of Honor, Q Who, Measure of a Man, Where Silence has Lease, Contagion, The Royale, Time Squared, Pen Pals, The Emmisary, Peak Performance are all favorites of mine. Even most of the lesser episodes of season 2 aren't that