I haven't seen a thread like this in ages, so I thought I'd make one.
I actually made a video of my top 20 favorite episodes so feel free to watch that instead of reading the written list
http://www.youtube.com/watch?v=KJlkywoGSAs
20. The Defector
Fantastic mix of intrigue, mystery and pathos
19. Tinker, Tenor, Doctor, Spy
A great concept leads to great comedy and some added understanding and sympathy for the doctor.
18. Cause and Effect
This episode just has the "cool" factor, I don't get tired of the repetition or that tractor beam tractoring the ship right into Enterprise's nacelle.
17. The Magnificent Ferengi
Probably the funniest comedy episode of Trek for me, I just loved the Ferengi whenever they appeared
16. Prey
The tension and dissention between Janeway and Seven in this episode felt so refreshing to Trek in general. "You Will Fail" is probably one of my favorite delivered lines in Trek.
15. The High Ground
I loved that it tackled an actual issue head on and in a clear way, something I really appreciate about season 3 TNG
14. Inter Arma Silent Enim Leges
This is the kind of story we all wish we could write, the twisty story really reflects the complexities of the Romulan Empire
13. Muse (VOY)
A beautiful episode inside and out. The story was unique, the set decoration was beautiful and the execution sublime.
12. Blink of an Eye
Fascinating hi-concept sci-fi delivered very well, pity about the Doctor's throwaway line about his "son"!
11. Frame of Mind
High concept, twisty sci-fi at its best
10. Improbable Cause/The Die is Cast
This two parter really sums up the high drama and epic feel DS9 brought to trek
9. Lessons
I weep like a baby every time Picard thinks Neela is dead on the surface. Beautiful music, a great guest star and believable chemistry make this episode a stand out "romance" episode.
8. Sacrifice of Angels
Gave us the best space battling we'd seen yet in Trek and a very satisfying yet tragic conclusion to the season 6 mini-arc
7. Thine Ownself
I simply loved the whole concept of this. Helps not to overthink this one though!
6. In the Pale Moonlight
Ah, the DS9 classic episode. Good helpings of Garak help any episode rise the list!
5. Dark Frontier
What really elevates this episode are the Hansen diaries. Seeing Anneka as a child in the flashbacks in the care of her reckless parents always gives me a lump in my throat knowing their eventual fate.
4. Lower Decks
Another episode that makes my eyes water, starting from that whistle going off for Picard's announcement at the end. I enjoyed the risks they were taking in season 7 and this was the one that paid off the most.
3. Before and After
Time travel is great when done well and Kes was the prime Trek candidate for a fantastic time travel episode. It really has everything you could need in a time travel episode and felt like a great pre-encore for the character.
2. Barge of the Dead
Roxann Dawson really was one of the most believable actors in all of Trek for me and given some really dramatic material and a highly inventive plot, she succeeds fantastically.
1. Trials and Tribble-ations
Its just what Star Trek is about in the end - fun and escapism and in the case of this episode, we get both in bucketloads. If this episode doesn't bring a smile to your face, you have a heart of stone!
So please share your favorite 10 or 20 (or more) episodes with me!
I actually made a video of my top 20 favorite episodes so feel free to watch that instead of reading the written list

http://www.youtube.com/watch?v=KJlkywoGSAs
20. The Defector
Fantastic mix of intrigue, mystery and pathos
19. Tinker, Tenor, Doctor, Spy
A great concept leads to great comedy and some added understanding and sympathy for the doctor.
18. Cause and Effect
This episode just has the "cool" factor, I don't get tired of the repetition or that tractor beam tractoring the ship right into Enterprise's nacelle.
17. The Magnificent Ferengi
Probably the funniest comedy episode of Trek for me, I just loved the Ferengi whenever they appeared
16. Prey
The tension and dissention between Janeway and Seven in this episode felt so refreshing to Trek in general. "You Will Fail" is probably one of my favorite delivered lines in Trek.
15. The High Ground
I loved that it tackled an actual issue head on and in a clear way, something I really appreciate about season 3 TNG
14. Inter Arma Silent Enim Leges
This is the kind of story we all wish we could write, the twisty story really reflects the complexities of the Romulan Empire
13. Muse (VOY)
A beautiful episode inside and out. The story was unique, the set decoration was beautiful and the execution sublime.
12. Blink of an Eye
Fascinating hi-concept sci-fi delivered very well, pity about the Doctor's throwaway line about his "son"!
11. Frame of Mind
High concept, twisty sci-fi at its best
10. Improbable Cause/The Die is Cast
This two parter really sums up the high drama and epic feel DS9 brought to trek
9. Lessons
I weep like a baby every time Picard thinks Neela is dead on the surface. Beautiful music, a great guest star and believable chemistry make this episode a stand out "romance" episode.
8. Sacrifice of Angels
Gave us the best space battling we'd seen yet in Trek and a very satisfying yet tragic conclusion to the season 6 mini-arc
7. Thine Ownself
I simply loved the whole concept of this. Helps not to overthink this one though!
6. In the Pale Moonlight
Ah, the DS9 classic episode. Good helpings of Garak help any episode rise the list!
5. Dark Frontier
What really elevates this episode are the Hansen diaries. Seeing Anneka as a child in the flashbacks in the care of her reckless parents always gives me a lump in my throat knowing their eventual fate.
4. Lower Decks
Another episode that makes my eyes water, starting from that whistle going off for Picard's announcement at the end. I enjoyed the risks they were taking in season 7 and this was the one that paid off the most.
3. Before and After
Time travel is great when done well and Kes was the prime Trek candidate for a fantastic time travel episode. It really has everything you could need in a time travel episode and felt like a great pre-encore for the character.
2. Barge of the Dead
Roxann Dawson really was one of the most believable actors in all of Trek for me and given some really dramatic material and a highly inventive plot, she succeeds fantastically.
1. Trials and Tribble-ations
Its just what Star Trek is about in the end - fun and escapism and in the case of this episode, we get both in bucketloads. If this episode doesn't bring a smile to your face, you have a heart of stone!
So please share your favorite 10 or 20 (or more) episodes with me!