^Well, it's not as if "The Doomsday Machine" is a particularly deep episode. It's basically TOS's special-effects extravaganza, a story driven mainly by action and spectacle over story. If you ask me, the only thing that makes it work is Sol Kaplan's fantastic musical score. If it had been tracked with stock music instead, I don't think it would have anywhere near the same reputation.
Or maybe people like some action and spectacle.
As for the story - well - the episode was nominated for a Hugo award. However, I won't speak to the criteria used for the nomination. Fans also seem to really like
Balance of Terror, too,
a lot. The music of
The Doomsday Machine is memorable, but that's not why I like the episode so much. I personally like it just because it's a space battle, and it was pulled off without getting too cheesy. It's a nice change of pace.
Fighting a giant robot in space is also an intriguing concept. Kirk's hypothesis of the backstory is fascinating, beyond the subtext of Armageddon, and raises some interesting unanswered questions (that I prefer to remain unanswered) with respect to exactly who was fighting the war.