Almost all of them have something for me. I'm very nostalgic about Season Two, largely because it was the only one I owned in full on videotape back in the day, so I watched it over and over again!
Of particular note I'd say I love Where Silence Has Lease (spooky atmosphere), Measure Of A Man (for all the usually stated reasons), Q Who (see previous entry), The Royale (again with the off feeling, love the bizarre mystery aspects), Peak Performance... I could go on. TNG Season Two struck just the right balance for me between the 'freshness' of Season One, and the more confident style that it would carry through to subsequent seasons.
Of course, I'm not blind to it's flaws. The Oirish one was terrible, and Shades Of Grey... well, I'd like to read a spirited defence of that one. I could never write such a defence, though.