I won't list a top 20, because I've not seen them all, and it's been a few years since I saw the early ones and many years since I saw the middle seasons. I will mention a few that I like a lot though:
Chain of Command - explored its theme very well, interesting to have a different captain, Troi gets her uniform, and David Warner!
Power Play - another good Troi episode?
Lessons - maybe the best romance episode in Trek. I don't think I've seen Patrick Stewart better.
Lower Decks - really interesting, nicely structured and rather moving. I like these episodes where the action happens off-screen and it focuses on the characters!
Parallels - Worf/Troi! Flat-out great in every respect.
Gambit - very entertaining. And with Caitlin Brown!
Genesis - OK, I haven't seen it since I was about 12, but at the time I found it very scary!
Chain of Command - explored its theme very well, interesting to have a different captain, Troi gets her uniform, and David Warner!

Power Play - another good Troi episode?
Lessons - maybe the best romance episode in Trek. I don't think I've seen Patrick Stewart better.
Lower Decks - really interesting, nicely structured and rather moving. I like these episodes where the action happens off-screen and it focuses on the characters!
Parallels - Worf/Troi! Flat-out great in every respect.
Gambit - very entertaining. And with Caitlin Brown!
Genesis - OK, I haven't seen it since I was about 12, but at the time I found it very scary!