The Magic has Lumiere's whilst the Wonder has Triton's. The other two main restaurants (Animator's Palate and Parrot Cay) are the same. In addition I beileve that where the Magic has Topsiders on Deck 9, on the Wonder it is called Beach Blamket Buffet, though I think the food and style is probably the same, certainly at lunchtimes.
The Magic is decorated in an Art Deco style while the Wonder is Art Nouvueax (sp?).
I'm sure others can supply more differences.