DMG has some advice on variants of the base core classes and on making your own with the witch as an example.
D20 modern has neat stat based classes (strong hero, charismatic hero, smart hero, quick hero, etc.). A little different base from D&D (action points, base classes only go to 10, etc.).
Call of Cthulhu has customizable pseudo expert classes.
Wheel of Time has a bunch of classes. They have a defense value which is different from D&D and a different magic system.
Diablo has a few but with lots of balance and mechanics problems particularly in their paladin class.
Dragonlance Campaign setting has the mystic.
Star Wars has a bunch but they use VP/wounds I believe.