Best - Ditto's Mysterious Mansion: Team twerp anyone? Duplica was awesome here, a lot better than that Johto episode. Who doesn't adore Ditto?
Worst - Who gets to keep Togepi?: I could be very biased and pick any of the episodes where Misty expressed her aversion towards Ash, but this episode wins. I hate it when people say that Misty mellowed down after winning the pipsqueak when in fact she didn't change at all until The Johto Journeys. Plus, she didn't deserve Togepi when she played no part in raising it prior to hatching.
Best - Pikachu Re-volts: Team Rocket siding with the twerps was very honest here. And the Japanese soundtracks of Mewtwo Strikes Back (and not the awfully dated American counterpart!) made this episode epic.
Worst - Wherefore Art Thou, Pokémon?: Misty's nastiness was so unbearable here. Shell Shock! and Pokémon Food Fight! are second.
Best - The Psychic Sidekicks!: Childhood favorite. And Team Rocket's mechanical ghost was a reflection of their pure genius!
Worst - Love Totodile Style!: That awful Azumarill is a self centered douchebag. Admittedly, the DP remake was better than this junk. The Fortune Hunters is another episode I can't stand because of Misty's nasty attitude, and Illusion Confusion is a sexist episode due to Hoothoot having a problem with Ash.