I have no real favorite episode...but there are a few that I really like.
As far as pok?mon capture/evolution, there's:
Challenge of the Samurai, Here Comes the Squirtle Squad, Sparks Fly for Magnemite, Attack of the Prehistoric Pok?mon, Good 'Quil Hunting, Goin' Apricorn, Tricks of the Trade, Hassle in the Castle, Control Freak, Entei at your own risk
as far as battles go:
School of Hard Knocks, Electric Shock Showdown, The Punchy Pok?mon, Volcanic Panic, First Round Start!, Fourth Round Rumble...