I would definitely have chosen Similitude for ENT, and In a Mirror Darkly, despite my dislike for the rest of S4.
For Voyager, I would definitely not have chosen Equinox. Janeway was PMS'ing so hard in part 2 that I assumed she'd been possessed by an alien entity. The Void was ok, but not near one of the best. Year of Hell and Timeless would be my top picks. Both amazing.
Good choices for DS9 and TNG. Can't argue with those.
For TOS, I mostly agree too, although I wouldn't put BoT quite so high. Still near the top of TOS, but not the best. COTEOF is easily the best TOS episode imo, and I think Tribbles deserves its place too. I'd probably choose Amok Time for second place from TOS.
I didn't actually read the list, because with over 700 episodes, they're bound to miss episodes I think should be there, and include ones I don't agree with.