Dark Sun- magic-users are powerful and very dangerous... and also hated by everyone else, mostly because their magic comes from sapping the life-force of living things. Wizards are largely responsible for Athas being mostly a giant desert. Here's more info http://athas.org/products/ds3
So, er... what's wrong with Ars Magica?
No problem -- very minor retool of Ars Magica -- simply remove the Code of Hermes, the Church and the social restraints of the Gift.
At that point there would be no contraints on the magi and they would rule everything in a New York minute...
The Hyperborea setting of Conan tends towards this sort of thing.
The world of Fafhrd and Grey Mouser also has its share of mysterious, godlike magic-users. Well, two of them, mostly.
It's modern-day, after a fashion.

(Dungeons & Dragons)
Rulebook featuring "high magic" options, including a host of new spells.