Personally I've gotta give it to WarioWare Gold. Love the whole 'Wario is broke and sets up a major sporting event while going more and more crazy' plot, and the character subplots were fun too. Wario Deluxe was an excellent way to end it too.
Get It Together was pretty neat, given it had the characters themselves appear in one overarching story, but the individual character stories mostly felt non-existent, with the possible exception of Pyoro.
WarioWare Move It was neat, though I'm not sure I cared much for the 'Wario becomes a volcano' thing.