Exactly what the title says. I'm not counting Generation I, 'cause Team Rocket didn't have a special battle theme back then. I'm also using the regular Team Rocket Battle Theme for Generations II and IV due to that being the music when you faced Archer, as well as Giovanni in the event battle of the remake.
Oh, and here are the themes themselves.
Generation II: Team Rocket Battle Theme
Generation III: Team Aqua/Magma Leader Battle Theme
Generation IV: Cyrus Battle Theme
Generation IV: HeartGold/SoulSilver Team Rocket Battle Theme
Generation V: Geechisu Battle Theme
My personal favorite would have to be the Cyrus theme. It just gives off this feeling that this guy is going to destroy the entire freakin' world unless you stop him. It's also fittingly eerie, given his stoic and emotionless character. The Team Aqua/Magma Leader theme is a close second.