I believe the OP was asking about any consensus list out there, not our personal top 5s.
From what I've seen here and elsewhere, The City on the Edge of Forever, The Doomsday Machine and Balance of Terror are generally considered to
be the top 3. Following those is a whole plethora of episodes including Corbomite, The Devil in the Dark, Journey to Babel, Mirror Mirror, The Cage, and several others.
Interestingly, there was a "Viewer's Choice Marathon" in 1991 that claimed to have compiled the top 10 episodes based on fan voting. I have no idea where/when this voting occurred or who was sampled. That top 10 was:
10. Balance of Terror
9. A Piece of the Action
8 & 7. The Menagerie
6. Space Seed
5. Amok Time
4. The Doomsday Machine
3. Mirror, Mirror
2. The City on the Edge of Forever
1. The Trouble With Tribbles
The Nimoy and Shatner introductions to the episodes:
http://www.youtube.com/watch?v=saAlrKGUWJ4
This list always held a special place in my heart because it was the first time (as a 7 year old!

) that I recorded Star Trek episodes for posterity. It was on KPTV12 (Portland, OR) for me!
And, just for kicks here's my personal top 5:
1. Balance of Terror
2. The Cage
3. City on the Edge of Forever
4. Mirror, Mirror
5. Space Seed