I'm one of those who like dougo speculated that if not an actual Cylon agent, Baltar is likely the incarnation of the Cylon god. Although I should clarify that I believe the "Cylon God" to merely be a self aware intelligence, and not much more. Which leads me to believe that Baltar was probably the initial attempt of the Cylon intelligence to embody itself in human form, but because the intelligence had grown so vast, the attempt (sort of) failed. Where we get the product, an extremely intelligent albeit deranged Baltar. Therefore this necessitated the creation of the 12 models, each with certain aspects of the Intelligence, and all able to work towards achieving the Cylon agenda. However as we see in the series, some of the models are "too perfect" replica's of humans.
Which also lends me to think that if Baltar did turn out to be human all along, that would be an incredibly cool story arc. As it is through a human the Cylon agenda (aside from the irony that Cylons need humans to procreate [another agenda of the cylons]) is achieved.
Either way, he makes for an extremely interesting character.