There's a difference between the Best of and my favorite episodes. I agree with almost everyone that's gone before about Best of, so I'll just suggest some of my favorites.
Haunting of Deck 12 - closest thing to a ghost story (and much better than Sub Rosa from TNG)
Tinker Tenor Doctor Spy - Simply for the Doc's opening song!
Scientific Method - "These lab rats are fighting back" It was one of the earlier Seven Saves the day episodes, so it didn't bother me as much as the later ones.
Q2 - because 2 Qs are better than one! (and Q and the Grey is meh)
Haunting of Deck 12 and Q2?
I think I just puked in my mouth