Here are the ones I always skip when I re-watch my DVDs:
For TNG, its Sub Rosa, Genesis, Justice, Shades of Gray, Journey's end, Angel 1, and pretty much any "trapped in the Holodeck episode."
Dor DS9 it's Meridian, Field of Fire, Profit and Lace, Let He who is without Sin, The Muse.
For VOY, its Fair Haven, Spirit Folk, 1159, The fight, and pretty much 3/4s of season 7.
ENT it's A Night in the sickbay, Terra Nova,These are the Voyages, Unexpected, Shuttlepod 1, Dear Doctor.
But all you TNG era haters, or people who cry and cry how B&B "screwed Trek up," the truth is you all can't handle the fact that some of the worst episodes came from TOS. 1960s or not, that's no excuse for bad TV.
Sure, it was the first. Sure it is the template for all that followed. Sure it had some pretty awesome episodes and movies that followed. Sure, maybe they have the best main characters, but as a whole, if you are really honest about it, TOS was the most uneven series and also had the most amount of bad episodes by percentage of total episodes, especially when you take into consideration it was the shortest show, with the highest percentage of crap. It even beats Enterprise, percentage wise.
Namely:
The alternative Factor
And the Children Shall Lead
Charlie X
Miri
Turnabout Intruder
Cat's Paw
Spocks Brain
Shore Leave
Return of the Archons
Mudd's Women
Wolf in the Fold
The Apple
Return to Tomorrow
By Any Other Name
A Piece of the Action
A Private little War
Omega Glory
Spectre of the Gun
Plato's Stepchildren
Lights of Zetar
Requiem for Methuselah
The Cloud Minders
Wink of an Eye
The Mark of Gideon
The Savage Curtain
That is over 1/3 of total TOS episodes, that are completely unwatchable, folks.