Yep, that Dominion war and its build up was the thing that embeded DS9 in second place for me. I just love war and Star Trek!!!
I agree that TOS was cheesy, but I found it was full of vigour and originality that the other series' (except Enterprise) can only build on. It was a bit stiff, and a bit over acted, but it's still a classic. I think that captain Kirk more or less made Star Trek, as the pioneer of the series he's a benchmark of respect and legend in both the Star Trek world itself and the Trekkie world. And the fact that the scenery was more or less all cardboard and paper mache (spelling?) made it all the more fun. Add to that some fun rivalry, a 30-45 minute love affair involving the captain in a good amount of the shows and some decent comedy and you've got a winner there. The atmosphere in TOS is great. When I first watched it (sometime in 1992/3) it was airing Wednesday evenings on the BBC. It was gripping and scary, you could almost believe it to be real. Since I've grown older and watched it over and over, the effect was still there. DS9 has this great atmosphere too, but not as much. I just don't feel this in TNG, it feels too rigid and 'rehearsed' for my liking.
I think the problem with TNG (for me) was that it seemed a little stiff, a little humdrum. Y'know, kinda like when you're sitting in a room full of computers, and the room just feels dense. I dunno, it just didn't make me think 'wow'! When I watched it. Don't get me wrong, I still liked it, as with all the series, but to me it doesn't compare with TOS & DS9. Gotta admit tho, it more than helped make Star Trek almost a household name.
Anyways enough from me. This is probably the only subject that I would be willing to write pages on!!!