One of my favorites is Doctor Gotham from the Shadowpact series; I feel he should be a Batman foe.
He's a warlock who was "buried" in the area that will become Gotham City! Awakened 3000 years later, he names himself Dr. Gotham after city.
He gains his powers from hundreds of mystic artefacts stored in an extra-dimesional space in his cloak. It's suggested that his dark magic may have twisted Gotham and it's inhabitants.
From B:tbtb, we have:
Fun Haus (long needed toy-themed villain)
Babyface and his gang (I think he's new)
Who knows what vilains will be introduced in Beware the Batman?