I agree with Jon about the thoughtful plotting of TNG but I've always had a soft spot for DS9. There was something about the constant struggle in Deep Space 9 that made if my favorite of the Star Trek series.
My favourite has always been Star Trek Voyager, mainly because it was the first series I ever saw. I also like the journey home. It is the first series since the original there they really are going where non one has gone before, and they are going it alone.
I enjoyed both Next Generation and Voyager, but I must say I really enjoyed some of the fun stories they had on Deep Space Nine. I loved Quark and Odo and most of the characters, but thought the Ferengi stories were particularly good. I had no expectations of the series, I saw it last year on dvd after watching the other two series and absolutely loved it.