Mario & Luigi: Dream Team
I recently finished up this game. As a big fan of the previous entries in the series that I've played, I really didn't mind the much-maligned tutorials much, and I found the game to be a lengthy and wholly charming adventure. Two of the Giant Luigi boss battles in particular stuck out to me.
The first of these is the epic struggle against the Zeekeeper.
These Giant battles consist of stylus attacks and dodges and gyroscope sections. When the Zeekeeper attacks, you have to dodge out of the way or send his attacks back at him. The real fun starts though when he rips open a tear in the dimensional fabric (!) and you have to dodge his attacks using the gyroscope and hit him when he's dazed. It doesn't hurt that the music in this battle is epic.
http://www.youtube.com/watch?v=mV6r-aMBvlk
The Giant Bowser battle is even more epic in some ways.
God DAMN, this battle was a real nail-biter for me. Unlike the non-Giant battles, there's no leveling up for Giant Luigi, so the battles increasingly put your skills to the test and there's no grinding to be done to help you increase your stats and give you a better chance in these battles. You fight Giant Bowser in the middle of a volcano (of course!) and he starts out charging against you. If you dodge him, he falls into lava. The goal is to keep knocking him into the lava, but it's not very easy to do so. You also can jump away from his attacks, onto his airship, and charge into him, and an army of Shy Guys will try to poke at your feet and serve up delicious, regenerating meat to Bowser. There's also a second phase requiring traversal on a massive Star across a gyroscopic obstacle course to deliver a finishing blow. Oh, and of course if you dodge an attack successfully, you get to execute that ultra-satisfying Bowser tail spin, a la Mario 64. The whole game is bursting with creativity--truly the Mario 3D World of RPGs--and these battles are an excellent example of this.
http://www.youtube.com/watch?v=vDDuh0gVj-c