The security issue with simple hashing (md5 et al) isn't really the speed, so much as the fact that it's idempotent; two different people with the same password will have the same hash, and so if one person's hash is brute-forced, the other one will as well. This facilitates rainbow attacks. Simply slowing the hash down isn't a very useful tactic for improving security. It doesn't matter how slow and cumbersome your hash algorithm is - as soon as someone has a weak password that's in a dictionary, EVERYONE with that weak password is vulnerable.
Also, hash algorithms such as md5 are for the purpose of generating a digest and checking if two things are probably the same as each other; they are not intended to be impossible to generate a collision for. Even if an underlying password itself requires a lot of brute forcing to determine, that doesn't mean it will be impossible to find some other bit pattern that generates the same hash in a trivial amount of time.
As such: please, please, PLEASE only use salted hashes for password storage. There is no reason to implement your own salted hash mechanism, either, as crypt() already does an excellent job of this.