I'm planning to use jBCrypt for password hashing in a new web application, as it is supposed to be the best from what I've read. As I haven't used it before I'm looking into if there is any reason not to use it.
I have this:
jBcrypt is probably fine as a crypto algorithm for your passwords; blowfish is relatively strong. Although there have been some reported implementation flaws in Blowfish itself, I don't find anything much reported about jBcrypt. On the other hand, Blowfish hasn't been tested nearly as heavily as other algorithms have, and a crack-style known-plaintxt attack often works better than expected, surprising crypto geeks.
So here's what I'd suggest: