I looked through the thread, and it seems like this hasn´t been mentioned yet: The Secrets Of The Immortal Nicholas Flamel by Michael Scott. Like AF, its basic settings build upon the human tendency to misunderstand things, transforming magic, etc. to 'stuff of legends'. It hasn´t got the sarcastic/witty remarks that´re constantly seen in AF, but if you´ve got as much as a basic historical knowledge, you´ll recognize a few characters over the course of the series. So far there´s four books - The Alchemyst, The Magician, The Sorceress and The Necromancer, but a fourth, The Warlock, will be available in a few days.
And I support those who mentioned Skulduggery Pleasant - it does have a whole lot in common with AF.