Out of all the episodes I found "Gotta Catch Ya Later" to be the most dampening. Misty's goodbye came with a depressing range of emotion and an equally depressing parting, which I'm glad was accentuated - despite that I don't like that Misty left the main cast, it added drama and emotion to the series in a way that none of the Johto episodes did otherwise for me (despite that I feel the dub is a tad more sappy in comparison to the morbidness of the original Japanese version). Butterfree's goodbye is quite good as well, and the expression on Ash's, Misty's, and Brock's visages calmly reflect the change of events in that episode (as well as the calm in their faces reflecting it all).
Pikachu's Goodbye is very emotional as well - it adds a pensive quality and depth in tone that most other episodes don't. I was surprised when Ash reacted the way he did. It's very, very good, though I do think the dub once again made it a bit too sappy. But a great episode nontheless.
As for the Dustox episode, I can't find myself affected emotionally by the dub due to excessive strain in the VA's voice. In the Japanese version, there's a certain terseness of emotion in the Seiyuu's voice that makes the scene that much more emotional for me (and highlights the "by one's lonesome and parting" quality of it).
But as stated, I'd give it to Gotta Catch Ya Later. As for Pokémon movies..... dunno why, but I felt very moved by the the Power of One (Pokémon 2000). Something about the score in both the dub and the Japanese version works very well for me. Then again, I feel similarly about Pokémon Heroes, Lucario and the Mystery of Mew, and Pokémon 4Ever, but if I had to choose, it'd be Pokémon 2000.