I can't really put my finger on anything specifically from the prequels I liked. I guess some of the ship designs were kinda cool, and Darth Maul wasn't so bad.
However, as others have pointed out, the parodies and deconstructions of the prelogy make them worth it in my opinion. The resurgence of interest in Star Wars is another plus. The Clone Wars series was somewhat redemptive of some parts of the prequels, but movies shouldn't rely on a later TV show, or books, or video games to make them solid. But I digress...
John Williams's scores were pretty fantastic, as always, especially Duel of the Fates and the Mustafar battle piece.