This is actually a very difficult question for me to answer because the more I think about it the more episodes I'm thinking of that were so good ffff
My all time favorite has to be Go West Young Meowth. It was the episode that really sold me on Meowth's character, never looked at him the same way again. ;o;
I really can't remember the name of the episode to save my life, but I know for a fact that involves large Tentacruel destroying one of the cities. I had the episode on VCR when I was about 6-7, and was my source of entertainment during a category 3 hurricane (we used a generator because we lost power, thus I was able to watch it).
I also love the Butterfree episode. 'Twas quite sad.
Pikachu's Goodbye, I think. It fills viewers up with emotion, and I loved it! It also shows the true bond between Ash and his Pikachu when he refused to go live with his own kind. After that one, I think I would have to say the last three episodes (Indigo League) with Ritchie in them.