Well, this isn't so much a prestige class as an alternate base class, but I like the flavor and crunch enough to plug it anyway.
The
Blue Mage
Background:
Nobody knows exactly what distinguishes those with inherent magical talent from those who lack it. Certainly the best magic users are smart or strong-willed, but just having those traits isn't enough. This question fascinated the Yuan-Ti, who attempted to solve this by artifically granting magical abilites to human test subjects.
The experiments at first seemed to be an overwhelming success. The subjects displayed the magical test characteristic (the ability to change their clothing's color, like genetic engineers do with glow in the dark stuff), and in addition had a small ability to cast spells.
There was only one problem - the magic given to the experimentees was formless, and they could not change it themselves to learn new spells. The dangers inherent in the experimental process, combined with the invasion of the Formians/Oni, lead to the research group's dissolution. The Yuan-Ti needed all their technomancers working on the magestorm and anti-outsider defenses.
It was only much later that it was discovered that the formless magic could be given form by external sources.
Group/Organizations
Similar to sorcerers, Blue Mages on the whole aren't very organized. There are loosely-net groups, and many people know a guy who knows a guy who can find someone who can cast a spell for (or on) you. Since blue magic is inherited, many blue mages learn at their parents' feet. Those that don't are often apprenticed or teach themselves. (Self-taught BMs are probably pretty rare, depending on plentiful magic items are)
Some clerics (Don't know which religions you're using) dislike them, claiming that their imitation of clerical magic usurps the powers rightfully only given to gods. [plot hook ahoy!] (note that a decent sorcerer disguise for a BM is only a spell-component pouch away.)
(Tie in - perhaps some of the magical races were the results of other experiments. Or at least owlbears were.)