Although I "know" that DS9 is superior to TNG in many way, I just can't make room for it over the Ent-D crew as my favourite show. I guess TNG came along at just the right time for me growing up, and the characters and actors in that show meant so much to me and gave me somewhere to escape to when things were bad. TNG will always be special to me.
1: TNG Wins overall for having the best characters, the most variety of stories, and having some of the individual best episodes in the whole franchise. Really if not for Picard, Worf, and a few key episodes, I'd put TOS ahead. Downsides are the first two seasons and too many new aliens that aren't really unique. As far as aliens go, they don't have enough Vulcans. Also, this is where the Klingons kind of became annoying with their mystical viking samurai thing...a little simplistic at times. 2: TOS Characters are almost as good as TNG, but we simply don't get to know all of them as well. Some of the stories were really cutting edge in the 60's, and even the ones where TNG completely copied the story are usually not as good. Downsides: if only it had gone a little longer and re-explored some of the things that earlier episodes established. A little more in recurring species would have been better than some of the similar plots. 3: DS9 What to say that hasn't already been said? I like that they had the balls to do half the things they did, and even in the more one-off episodes, they have some real winners. Characters are a mixed bag. Sisko, Bashir, Odo, Garak and even Quark add a lot to the show. The rest of the characters are a bit more of a mixed bag. Downsides: some of the individual episodes are really bad. Even if they aren't completely terrible, they can be boring. There are also a lot of implausible things big and small - Ducat's final story arc, ships flying right next to each other (space is a big place and the ships move really fast even at impulse, after all), phasers causing minor wounds, and so on. 4: VOY To be fair, I haven't seen that many, but it has lots of good things going for it. Some of the places they go actually are really good looking, and the episodes so far are a lot of fun. Characters aren't terrible, but a few are uninteresting. I like Janeway, Neelix (yes, seriously), the Doctor, even Paris and Chakotay in their own way. Chakotay's Indian stereotypes are annoying, but he does come across as a competent 1st officer. Downsides: Well first off there are just things that make no sense. They were writing TNG plots when they should have been doing their own thing. I think it's obvious that, by this point, the science is thrown out the window. 5: TAS I haven't watched it yet, so it gets next to last. We'll just have to wait and see. 100th place: ENT Pros: the sets look good. Cons: the characters are all awful and one dimensional. The aliens are all completely ridiculous. The plot forces the characters to do things that make no sense. They made a prequel just so they could rehash pre-established species as new, but they do it in a terrible way every time. The things that it does introduce are almost all stupid. I think Klingon ridges as the plot for an entire episode pretty much sums up the series.