I picked up Mario and Luigi: Bowser's Inside Story for the DS the other day. I'm a big Bowser fan and this is his first spin-off game, despite being an entry in the Mario RPG DS series: Mario and Luigi. The game is pretty good, you actually play as Bowser a fair bit more than Mario and Luigi. At any given time in the game you can control all three, it works basically so that Bowser is on top while the boys are inside his body on the bottom screen, and you can switch back and forth through the A, B, X, and Y buttons (X and Y control Bowser, B is Luigi, and Mario is A).
Fawful is pretty awesome as usual "FAWFUL HAS FURY!"
apparently later in the game Bowser morphs into kaiju of Godzilla-like proportions and you dual-screen battle where you hold the DS on it's side and control bowser with the touch screen and stylus while the enemy is on the right (top) screen.