When I read the title of this poll, I thought it would be something else. Even within standard D&D, there are several systems of magic.
The most obvious difference is arcane vs divine magic. And within arcane magic, there's wizardry vs sorcery. For bards, there's the standard spell system vs the spellstrings that Monte's bard uses. In Rokugan, the divine vs arcane distinction doesn't seem very significant. Instead, spells are split into the four primary elements for Shugenja. Then there's the psionic system.
Outside of the core books, Wizards has publsihed some alternate forms of magic, including Rune magic and Gem magic in the Forgotten Realms.
Outside of Wizards, there are many alternate magic systems in the various d20 books, like Spells and Spellcraft by FFG, Spells and Magic by Bastion, and Magic by AEG.
As far as this poll goes, though, I abstain, since I'm only familiar with standard magic and psionics.