1. Gym Leader/Elite Four (bubanabubanaBUBANABUBANABUBANABUBANA.....BA....BA....BA....BA....BA.BA., BEST GYM LEADER THEME EVER)
I think Gen 4's Gym Leader battle theme (Sinnoh, not Johto/Kanto) is the simplest of all the Gym Leader battle themes - it doesn't change key or have any different tunes added to it, as with Gen 5's when the Gym Leader is down to their last Pokémon. It symbolizes what it's meant to be - a battle with the strongest Trainer in the Gym.
And we can all agree that Cynthia's battle theme is the most intense Champion battle theme ever, right? (I'd second it only to Lance's.)