Hmm. Incredibly hard for me to answer.
I can say for sure that it is not Enterprise which I found to be utter shite and it was not what I wanted the early days of Starfleet exploration to be (I had more of a Das Boot type image in my head and wanted the ship to be far more industrial) plus the bullshit title song, plus the bullshit gel that they had half naked characters rubbing in to each other after missions. Such shit.
I give TOS a respectful nod - it did not have the budget but what the Great Bird of the Galaxy did was amazing and ground breaking for its day and while some of the episodes are pure cheese, there are still some that are splendid Sci Fi. I have to salute it for being completely iconic.
TNG, in my mind, came out of the blocks with a dodgy first season. And much of the second season clearly suffered from a writer's strike at the time. I would not bother watching any of the first two seasons again. Later on it did hit its stride (and then fell on its ass with some of the movies). It was good sci fi but I don't know that as an entire entity I would rank it as great. Picard and Data were stellar. Troi was rubbish till they let Marina Sirtis put a proper uniform on and Crusher was pretty bland.
In contrast I do consider the first season of DS9 to contain some of its best episodes. There is a superb "bottle show" where Kira is interrogating a suspected war criminal (called "Duet") and the writing and performance was fan bloody tastic

But I did get pissed a bit when Worf came on board because he took time and plot away from Kira and Odo who were my favourites. I liked that there was conflict and I liked the story arc (but then I also adore seasons 1-4 of Babylon 5 and all of BSG). I didn't like the Dax replacement (and the true story behind that leaves a nasty flavour) and I didn't like the pairing of Odo and Kira at all or the marriage of Worf and Jadzia - don't much care for soap in my sci fi.
Voyager began with some interesting concepts and I do like Janeway as a Captain. To my mind it got powerful when 7of9 came aboard because there was this new conflict that I had expected to see between Maquis and Starfleet and been disappointed to find was not present. Yes Jeri Ryan as 7 is some nice eye candy (oddly, Jeri Ryan does little for me out of character) but there were some strong stories there. I liked that it had a proper ending (something I have never forgiven Quantum Leap for) although thought that who 7 ended up with was bullshit, utter utter bullshit. She should have ended up with Janeway =D
Each series for me has an "it is good but I wish X was different". And they appealed in different ways that I sometimes feel that the Star Trek lexicon/artwork/franchise is one of the only things that they have in common.
In terms of re-watch and thus faourites I guess I would go with DS9, then seasons 4-end of Voyager, then TNG and then TOS.