TOS: This is a tough one, that third season was a minefield of crap episodes. I was prepared for the crap that was Spock's Brain, And The Children Shall Lead and The Way to Eden, so the episodes which jump out at me as the worst are Plato's Stepchildren and The Savage Curtain. The Omega Glory and The Alternative Factor are also terrible.
TNG: I can forgive Shades of Grey because of the writers strike, so the worst episodes have to be in that awful first season; The Naked Now, Code of Honour and Angel One. Sub Rosa is bad, but is made to look worse by all the great episodes of seasons 3-6.
DS9: Let He Who is Without Sin and Profit and Lace may not be the worst episodes of the show, but they are terrible when compared to the general awesomeness of seasons 5 & 6. Meridian has a terrible A-story, but a good B-story rescues it.
VOY: Threshold.
ENT: I don't share the hate most people have for A Night in Sickbay, so the worst for me is easily Precious Cargo. That episode was bad in every way possible.
Overall: Threshold.