Battle Aboard the St. Anne used to be my favorite, but now my favorites are the early Johto Episodes. (Starts singing the Johto Journeys theme song)
I think the worst episodes are the Pokemon Advanced episodes. I watched the one where may gets her Wurmple confused with Jessie's, PURE CRAP.
Also, the stupidest quotes came from Advanced:
2nd stupidest quote: "All right, the brain freeze, my favorite part!" -Ash, while drinking a milkshake
Stupidest quote: "Being a fire type, Torchic doesn't want to go into the water." -Brock. It might not sound stupid to you, but seriously, I think that's the worst pokemon quote i eva heard.