I have to go with TNG, though DS9 is close.
Story: I would go with TNG over DS9. Yeah, DS9 would win for overall arc, but TNG had the best writing for individual episodes, IMO. DS9 fell back more on standard TV conventions a lot more than TNG did, and the only argument that it had better writing is that stories in episodes happened to be linked together more.
Special effects: Not that it affects my opinion of the show, but Enterprise.