Well. I saw how advanced this thread was just from the number of posts and thought it would either be over, or maybe I'd get to decide it. Ah, better that I don't.

Glad I can participate right at the end. Now . . .
"That's what the board is all about. That's WHY we're aboard it. You may dissent without prejudice. DO I HEAR a negative vote?"
Well, Captain . . . [meekly raises hand] uh, yes. Balance of Terror is an amazing episode whose flaws can really for the most part only be counted on one hand. I eliminated it from the S1 game based on the early-days confusion over the way in which the Romulan ship is powered. But that's a really grungy nitpick that is faaaaaar outweighed by thousands of good things, as are the other very small flaws.
Nonetheless, The Doomsday Machine is, has been, and always shall be my friend . . . and my favorite episode. Its flaws, to me, are virtually negligible. Some of you have mentioned William Windom chewing the scenery, but I don't find it overdone and I think Decker's survivor's guilt is moving. The planet killer effect as a giant space Bugle doesn't bother me in the slightest, but for anyone bothered by it, there's TOS-R, which took care of that issue for the most part and also added fantastic scenes of the Enterprise whizzing around firing its phasers like a Star Wars ship. Either the original version or the remastered version should - in my humble opinion

- satisfy just about everyone. The Doomsday Machine is also free of the recurring themes that sometimes turned up perhaps once too often - unless you count Kirk's defeat of the planet killer as Kirk destroying a computer, which I don't. There is no unstoppable alien species, only a relic of their possibly warlike culture. There's no love story for those who dislike that element. The Enterprise isn't completely neutralized; it fights back, and the poor Constellation is, poetically, the vehicle of the planet killer's destruction. And, I mean, if you're still watching a show made 50 years ago that you've seen about 100-150 times easy and STILL on the edge of your seat (as I am) during the final action sequence even though you know how it's going to turn out, you're probably watching something pretty good.
Balance of Terror - 3
The Doomsday Machine - 2