I'm an old school Ultraman fan who enjoyed this show immensely after school in the late 70s, and now I enjoy it still on DVD.
While it's hard to list an absolute number one (the episodes by Akio Jissoji are my personal favorites), I have to go with the first appearance of the Baltan as one of the best. These space prawns have been Ultraman's nemesis since the beginning and we see them here in their infancy, complete with that "Hra hra hra" laugh that has stuck with me since seeing them on tv.
This was the first episode that went into production and have viewed it in the original Japanese along with the English dub that I grew up with. I'm glad this wasn't the first aired episode, though. We needed some back story before with Hayata and the Science Patrol, first.
I found I was surprised at the subtle differences between the two. I assumed they changed things slightly to match the mouth movements to English better. But the story in Japanese is more sophisticated- at least for a kid's show. But here, Ide, or Ito as I knew him, seems like less of a ham in the Japanese and more the likable class clown. Hayata nearly falls to his death to get a hold of the beta capsule (which seemed like a gutsy move to me). But it's the Baltans here that are the stars. Their creeping about in the buildings and the way they disappear/reappear, as well as that laugh really freaks you out as a kid. Plus, you can almost sympathize with their plight- they just want a new home. Sure they're in the billions, but they're microscopic. They should have more to worry about us boiling them in a pot of water with some melted butter on the side more than anything else. But they get too nasty and Ultraman comes to the rescue.
The story is typical for the Ultaman canon, but the Baltans are top notch for an enemy. And fortunately, we get to see them again later. Now I feel like going to get some shrimp to eat....