Giovanni - World Domination Johto People - Bring back Giovanni Maxie and Archie - Fill the world with water/land Cyrus - Destroy the world then make a new one Ghetsis - World Domination through a more secretive method.
Team Rocket - Make lots of money, and that was it. That goal never changed even in Johto, though they later got desperate and wound up begging Giovanni to come back once their plans got FUBAR'd enough.
Team Magma/Aqua - Make the world either all-land or all-water. They weren't exactly concerned about collateral damage in their plans, though Groudon and Kyogre's power wound up being too much of a "good" thing.
Team Galactic - Erase the old universe and create a new one that Cyrus can rule. Yeah... that's a bit much.
Team Plasma - Steal every Pokemon in the region so that nobody gets any. All their talk of Pokemon liberation is actually a bunch of BS they made up to bamboozle Trainers into releasing their Pokemon, so they're essentially no better than Team Rocket.