On the Paragon Initiative blog there's a post showing you how to implement secure authentication with long term persistence (a secure "remember me" essentially) in a PHP application

A common problem in web development is to implement user authentication and access controls, typically accomplished through sign-up and log-in forms. Though these systems are simple enough in theory, engineering one that lives up to application security standards is a daunting undertaking.

Without a great deal of care and sophistication, authentication systems can be as fragile as a cardboard lemonade stand in a category five hurricane. However, for everything that can go wrong, there is an effective (and often simple) way to achieve a higher level of security and resilience.

He starts with a look at passwords - how to correctly hash them, how salts play into it and some suggestions about password policies. From there he gets into the "remember me" handling, giving two common problems with most systems: insufficient randomness and timing leaks (timing attack issues). He then proposes a different kind of solution, storing some additional information in the database record, a "selector" that's not timing dependent to find the record then use a timing attack safe method to compare the hashes. He ends the post with a brief look at account recovery and some things to watch out for if you plan to implement it.