scrypt is designed to be difficult on hardware. Both bcrypt and scrypt are currently difficult on GPU hardware, but it's unlikely to remain that way. Both are better than PBKDF2. scrypt is likely to be better longer. But really: throw a dart at any of the three of them.
It sounds like one of the Bitcoin alternatives is scrypt based, and they are putatively getting a roughly 10x speedup from GPUs: https://en.bitcoin.it/wiki/Litecoin#Scrypt_Proof_of_Work . Is that a new development, or is it in the neighborhood of how GPU-resistant it was supposed to be?
