1. DS9: I love it for its rich, character-driven stories as well as the ongoing storylines. For me, it's more complex and more challenging than any of the other Treks which is one of the reasons it's my favorite. I also enjoyed a lot of the humor as well, meaning it was a great mix overall.
2. TOS: I think one of the main reasons TOS comes second for me is the characters. It's just a lot of fun to watch Kirk, Spock and Bones in particular interact with each other, depending on each other while having their differences (and letting it show). I also really like the sense of adventure as well as the 60's feel.
3. TNG: This used to be my favorite Trek show back in the day. And I still enjoy some of the episodes (e.g. BOBW or AGT) as well as some of the characters (e.g. Picard or Crusher). However, I find most of the episodes really hard to sit through these days. Generally speaking, my perception is that the show tends to be too simplistic and formulaic a lot of the time. I also find the interaction between most of the characters to be rather uninteresting and (in particular when it comes to romance) rather immature.
4. VOY: I enjoy the Doctor a lot. He's easily my favorite character (plus I think Picardo is great). I also like the basic idea. But I don't like what they did with it. To me, the show simply felt like TNG part 2 most of the time. And I really missed the sense of the ship really being 'out there's as well as any serious kind of conflict aboard ship (which IMHO just should have been there). I also find the technobabble absolutely unbearable on the show. And, again, I find most of the character interactions to be rather uninteresting, with romances also being handled rather immaturely IMHO.
5. ENT: Another thread a while ago made me think about this show for quite a while. And I came to the conclusion that, simply and honestly speaking, there is nothing I find redeeming about ENT. That's why it's last.