Very good point, Light, I have often wondered about if his parents would return (particularly when we started Hoenn) and try again, and with the Battle Frontier stuff, I hope they do return.
But yes, for best character episode, that would be the one. The ending was quite touching.
My favorite for writing: Forest Grumps, the dub's third season finale. It wasn't anything on the twerps, but the Rockets as we see them actually reflect on their miserable lives (we never see this anymore in Hoenn) and wondering "would life be better if we quit Team Rocket right now?" Such insight into one's identity is quite rare (particularly in this series as it should have been done already, although James' musing with the Meowth cult one was a nice prelude), and interesting that the writers would toy with this, seeing our trio waver their loyalty to the corps.
It was Jessie's best episode with this reflection. The ending was the clicher as the implication of her misery caused by James and Meowth would spread through three seasons. The Rocketshipper material is finally returned in Season Seven and that's why I wish they'd do this type of character writing more often.
(Personal note: For those would say A Hole Lotta Trouble, don't, the episode had no emotional impact, although the James/Ash interaction was a nice start but died down quickly and James' emotional vulnerability annoyed. To Brock, okay, fine, he's empathic, but Ash? Please. If you're going to emote to an enemy, do it to one that can care about you.)