I have to go with DS9 with TNG a close second, and I hope we are talking about the televised finale, and not including Nemesis or TUC.
DS9 is a true finale, as it resolves almost every story arc, at least the ones that had not been resolved by that point. It is a true end to the DS9 story with the fate of Sisko left as a question. Too bad it was never revisited on screen, but at least the dialogue establishes he does plan to return.
TNG's finale was also great, but it doesn't really resolve the show...but then again it wasn't meant to. Seeing an alternate future, and revisiting the Q trial was a great concept and for its time, was ground breaking and innovative. And had that been the true end of the TNG story, it would have been great. Unfortunately, for me, Genesis and Nemesis both tarnish All Good things for me. FC and Insurrection are self contained enough that they don't, and besides having the Enterprise E, the stories were written in a way where they could have almost could have taken place during the run of the show. Genesis, besides being responsible for the death of Kirk (lame!), also was responsible for the death of Enterprise-D (also, lame!), That right there throws the monkey wrench into the possibility of its refit as seen in AGT. Nemesis, for obvious reasons (has it truly almost been 10 years, now since its release??!!) just gives the TNG cast a horrible send off. The only good thing that came out of it for me was Riker and Troi's resolution, in that they finally marry and Riker finally gets a command.
The reason I didn't pic the others:
TOS: Unless you are counting TUC, TOS never had a finale. It was just cancelled.
VOY: It really ended with no surprise...they get home. But because time travel is involved, and an alternate future, it just seemed like it was taking a page from the book of the TNG finale. I enjoyed it, but it just didn't seem as fresh and ground breaking, as TNG or DS9 finale. Maybe that is a microcosm and summary of the entire show? I don't know.
ENT: And finally, we have These are the Voyages. People actually picked this one? I suppose it really is just personal preference but, really? REALLY?????? Ugh, in my eyes, that was THE WORST idea for a finale, EVAR! Terra Prime was the true finale for ENT as far as I am concerned. I mean who's idea was it to bring in Fat Riker and Aging Troi for this, as if it is going on at the same time frame as the episode Pegasus, when they are clearly 11 years older? It MIGHT have worked as a generic episode, but as a finale??? The whole thing just smacks as an excuse for Frakes to insert himself into the show, just so he can say he was on all the shows, except TOS.
And, in the episode of The Pegasus, Riker is supposedly struggling with a decision that's about to impact the fate of Federation-Romulan relations and how it is going to impact his career, and he runs off to the holo-deck for a few hours, to re-enact the ENT crews final mission before the federation charter is signed? That's is bizarre. What if the viewer hadn't seen TNG or the Pegasus episode, either? They wouldn't get the reference.
Not to mention that it short changes the ENT cast, it isn't a finale for them, but relegates the last episode of ENT to actually being a TNG episode, and a sequel to a mediocre TNG episode, at that. TATV was a FAIL all the way around.