If one wanted to use d20, d20 Modern would probably be the best base. Pure Mortals could use the base classes without any modification: Minor Talents and the weaker Changelings/Scions, as well as any other supernaturals who are 'one-trick ponies', would still use the base classes, but simply with a template applied (with their weak powers balanced by minor weaknesses: for example, Changelings weak enough to use this setup would have one minor ability, either a very weak magical one, a weak bonus feat, or simply a bonus to an ability score, and would be vulnerable to iron; they might also suffer a penalty to certain social skills as they have less free will.)
For example:
Changeling (Minor) - Troll Born
*Bonus Feat: Toughness
*+2 racial bonus to Intimidate checks.
*Fae Vulnerabilities: A minor changeling without Damage Reduction suffers +25% damage (round up) from iron weapons. The troll-born also suffers a -4 penalty to one skill from the following list: Bluff, Diplomacy, Gather Information, and Sense Motive.
Or:
Minor Talent - Precognitive
* Future Sight: A precognitive gains a +1 competence bonus on Armor Class against attacks by mortal opponents.
*+2 competence bonus to Bluff and Sense Motive checks
* Bound by Time: A precognitive suffers a -2 penalty to all Charisma-based skill checks except Bluff.
* Council's Ward: A precognitive can be detected by Wardens and other members of the White Council who are within X feet. Any breaking of the Laws is detectable from a much greater radius.
Things like a Red Court Infected would be a template too, with greater bonuses and much greater penalties. The key would be: are the abilities greatly improvable by practice? Things that are (Wizard, Sorcerer) are classes; things that aren't (Red Court Infected), or are profoundly limited in how they can be improved (Minor Talent) are templates. I'm tempted to say that White Court Vampire is a class, since there seem to be greatly varying degrees of skill/power in the use of the vampire abilities, but it might be both (a template for the base abilities, and a class for refining the abilities.)
EDIT TO ADD:
Of the types we've seen so far:
Classes:
Wizard (Basic Class)
Sorcerer (Basic Class) - may be the same class as wizard with different options chosen
White Court Vampire (Basic Class)
Werewolf (Advanced Class - but with low prerequisites)
Faithful (Basic Class)
Faerie Court Knight (Advanced Class)
as well as the basic classes from D20 Modern, for plain mortals and minor talents...
Template:
Changeling (actually several templates depending on Fae parent)
Lycanthrope
Minor Talent (actually several templates depending on specific power)
Red-Court Infected
White-Court Born