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Electric Shock Showdown. To this day something about that episode still sticks with me. I think it's because back then the idea of a first stage taking on it's evolved, much stronger form, seemed like a real David and Goliath thing. Lt. Surge was also a bit of a scary guy. Another thing, Ash actually legitimately won his Gym badge in that episode.
I also really like the episode where the Pokemon gets separated from their trainers and we spend a whole episode with them trying to find them and us understanding what they're saying with subtitles. They really show off more of their personalities in that one. There needs to be more episodes like that in the franchise