Here's a big caveat: you cannot choose from all 51 episodes of the series, as you will notice from this list:
Ep 01: "Those Who Challenge The Sun"
We meet Ed & Al, they meet Rose.
Ep 07: "Night of the Chimera's Cry"
Putting 1 and 1 together with alchemy.
Ep 08: "The Philosopher's Stone"
Winry meets a chopper. It has nothing at all to do with motorcycles.
Ep 22: "Created Human"
Don't step in the red water!
Ep 25: "Words of Farewell"
Get too close to the sun and you will get burned.
Ep 34: "Theory of Avarice"
The Greed and Ed Showdown.
Ep 37: "Flame Alchemist: The Bachelor Lieutenant/The Mystery of Warehouse 13"
Things that are crack-tastic!
Ep 40: "The Scar"
How did Scar get his scar anyway?
Ep 42: "His Name is Unknown"
Scar's last chance.
Ep 51: "Laws and Promises" (Munich 1921)
The brothers' bond is tested.
Right away, fan-favorite Episode 13 ("Flame vs. Fullmetal") is missing. I also detect some other favorite episodes missing:
05: "The Man w/the Mechanical Arm"
17: "House of the Waiting Family"
19: "The Truth Behind Truths"
44: "Hoenheim of Light"
Since you can only pick one episode, I chose Ep 37. It's the only light-hearted episode on their list. Almost everything else is dark and brooding to a degree. At least 3 episodes on the list are those depressing episodes that will make you slit your wrists in anguish and depression. I love Episode 34 - it's definitely in my top 5 picks of all the episodes - but it's one of *those* episodes I just mentioned. (Yes, I cried at the end when they premiered Episode 34 at Nekocon 2005.)
Go and vote today! The results will be interesting to find out, to say the least!
(comments disabled as of 6:00pm ET 2/26/08 to minimize wank)