Over at Akratic Wizardry, Akrasia has published his Swords & Wizardry House Rules. Those house rules contain rules to modify the way magic works. Akrasia has re-categorized all the magical spells into three categories: white magic (in tune with the natural order), grey magic (manipulating the natural order) and black magic (contrary to the natural order).
I think Akrasia's approach is a sound one, considering his house rules are designed for a swords & sorcery style of game.
I also like the approach used in Avalon Hill's Magic Realm. In that game, all magic is divided into five colors.
White Magic - represents power from on high, working beneficial magic.
Grey Magic - represents natural laws, controlling nature.
Gold Magic - represents wood sprites, working elvish magic.
Purple Magic - represents elemental energies, twisting and reshaping reality.
Black Magic - represents demonic power, working infernal magic.
There are ten different magic-using classes in Magic Realm, and each has certain colors of magic available to them. For example, the White Knight and the Pilgrim both have access to White magic. The Elf has access to Gold magic. The Druid has access to Grey magic. The Wizard has access to Grey, Gold and Purple magic. The Witch has access to Grey and Black magic, and so on.
I will post a list of the spells in Magic Realm, by color, shortly.